When we cast off the mantle of an oppressive religious system, sometimes the prejudices ingrained in us over years' time linger after our belief in the gods or whatever we previously held sacred has withered away. One of the first agnostics I ever met was also unrepentantly homophobic.
In some settings, such as liberal religious communities like Unitarian Universalism, there is encouragement to cast off racism, homophobia, and intolerance of other religious communities. But the freethinker who chooses not to have any part of religion -- even a humanist-friendly sort such as UUism -- is pretty much left to unlearn these patterns of thinking on his or her own.
What to do? Well, not every area provides opportunities for meaningful multiracial activities or learning outlets such as PFLAG. For the rural heretic wanting to break free of mindless prejudices, the library is one of a very few lifelines to reality. (And in many small areas, it's not even much of one -- the more "progressive" books might have to be ordered through an interlibrary loan, an iffy prospect at best, leaving the seeker with the Internet as another tool to new ideas.)
There's a massive body of literature out there discussing the ascent of homo sapiens as we understand it now -- not as some nomadic people in a pre-scientific era thousands of years past dreamt it up.
For instance, a reading of Carl Sagan and Ann Druyan's Shadows of Forgotten Ancestors will help the reader realize that "race" as we commonly understand it is a lie, a myth, with little relation to reality. Differences in hair texture, skin pigmentation, eye shape and nasal structure are only surface traits; our similarities far outweigh our differences, so much so that type A blood from a "caucasian" is chemically the same as type A blood from an "asian" person. (And for those suckered in by the phony academics underlying books like The Bell Curve, many more books disprove the racist propaganda therein.)
Like racism, homophobia largely stems from erroneous assumptions about nature that are viewed uncritically as facts in our society. (One could also argue a bit of "protesting too much" behind the mentality -- and the historical case of gay-baiting US politician Roy Cohn, whose secret homosexuality came to light as he was dying of AIDS, one would be right.)
A quick look at the anti-gay rhetoric quickly reveals origins in the Jewish myth of Sodom and Gamorrah (an incident conspicuously absent from other, non-Hebrew, chronicles of the time period), a few passages of the Christian New Testament, or Islamic cultural mores (largely borrowed from Judaism) and, possibly, Qu'ran passages. At some point, deities are invoked in almost any anti-gay rant... making those arguments one hundred percent irrelevant to those of us who have put aside the idea of gods.
What about the argument that homosexuality is an "affront to nature," since it doesn't propagate the species? The wise person will ask, "So?" Plenty of sexual activities performed by heterosexual couples don't lead to pregnancy; it's not as if our species is underpopulated, either. If you take a purely reproduction-centric view of biological activities, plenty of things we do -- watching television, listening to music, drinking soda -- are not connected to reproduction; do we ban those activities as well? Besides, homosexual love isn't "all about sex" any more than heterosexual love is; there are gay couples who've been together for years. If people can find a lifetime of happiness together, I don't hate them for it -- as one of the lonely people, I envy them.
(And the notion that gay people are, by default, "promiscuous" is a foolish one. Were it not for oppression by "straight" society, gay couples would be able to be more open, like anyone else; this would relieve them of unimaginable pressure, and more couples would make it to long-term relationships. As society has grown more tolerant in some regions of the US, this has already happened.)
Finally, religious prejudice... that is, pure and simple, a throwback to one's earlier condition as a religionist. See, one of the (many, many) errors in logic made my many religions on a daily basis is that of stereotyping, creating a false "us and them" dichotomy. In reality, one's religious beliefs, or lack thereof, often have very little to do with one's relative ethical standing. Many people are "good" despite their religion, not because of it, and the same applies to those of us who are not religious.
I was raised in a conservative Christian household. In my adolescence and young adulthood, I've gotten to know Christians of almost all stripes and ideologies, from the most frighteningly fascist conservatives to the most amusingly flighty liberals. I've also met people of other religious traditions -- pagans, Jews, Muslims, Buddhists -- and those who espouse no religious beliefs at all. From my experiences in living and in meeting people, as well as the distance that my atheism allows me to take from "religion," I like to think I've gained some perspective on things.
First off, I've learned that not every Christian is a kind and loving neighbor. Some are, but there are plenty of mean-spirited, venomous, and petty individuals walking around wearing cross necklaces, filling the church pews, and working in Christian Coalition-backed election campaigns. On the other hand, there are Christians running thrift stores to feed and clothe the poor, helping Habitat for the Humanity provide homes for the homeless, and working in literacy programs to help give the undereducated a fair shot at life.
Second, I've learned that not every atheist, agnostic, or skeptic is an immoral lout; many try to hold themselves (ourselves) to a higher standard of conduct than those religious sorts who feel that their god is eagerly awaiting for them to come confess some new sin and give them absolution. Freethinkers have to live by their (our) own consciences, not some "divine" set of rules that wipe the slate clean once a week. On the other hand, some non-theists don't do enough thinking to deserve the title "freethinker," and some spend their whole existence wallowing in self-pity, making their complaint "Life is so meaningless!" a self-fulfilling prophecy.
Looking at other religions, I've come to know that Wiccans don't sacrifice animals, nor do Satanists; adherents of both religions tend to value life more than those subscribing to religions which preach that this life is a meaningless prelude to another. I've sent plenty of Jews who were more generous than Christians, and more than one Muslim who was more gentle of disposition. And those "wacky" Buddhists, Hindus, and Taoists can sometimes be more down-to-earth in their view of life than, say, a Jack Van Impe or a Benny Hinn.
Realizing that there is some good in the teachings of any and all religions -- even Christianity (or whatever you walked away from) -- doesn't mean sacrificing my intellectual integrity or letting my atheism slip. Not at all. Instead, I think that seeing the thread of humanism and humanity in all these faiths... even the nontheistic "philosophical systems"... speaks volumes about the innate potential we have already, without the need for any theoretical gods butting in.
But a very important step towards realizing that potential is overcoming traps such as false perceptions of various groups of people. When you see the people around you as individual human beings first, and as Hispanics or lesbians or worshippers of the Almighty Doorknob second, you make a tremendous stride towards being the best person you can.

God Is Dead -- Now What?