Religion isn't bad. People are bad. Never does it say "Love thy neighbour, unless they're gay, black or a woman. Burn them." In fact, I defy you to name a religion that actively discriminates like that. You can't use quotes, because gods don't write books, people do. Use rules.
A religion that actively discriminates? Christianity.
Please people aren't bad. Refer to the 'An Ethics Question' thread for clarification.
Christianity actively discriminates against gays, Wiccans, women and until recently, Jews. Gays are committing what the Bible calls a sin, and are thus thought of by many Christians as sexual deviants, and sometimes as little better than rapists. Many Christians believe, because of their Christianity, that HIV is a punishment by god for homosexuality. Christianity also calls Wiccans "witches" and witchcraft is punishable by death according to the Bible. Many Christian sects accord women different rights than men, and the Bible teaches the wife to submit to the husband, that women on their periods are ritually unclean, and includes many other sexist claims and proscriptions. Finally, the Catholic church, until recently, blamed Jews for the death of Christ. There is a long history of beliefs that Jews sacrifice Christian babies, drink the blood of Christians, etc. etc.
Islam is even worse than Christianity. Not only does Islam include all of the same sexist teachings as Christianity and then some, all of the same anti-homosexual teachings and then some, and different but equally vicious anti-semitic teachings, it also places a death sentence on every single ex-Muslim. If you have the bad luck to be born to Muslim parents, and then realize once you are old enough to think for yourself that Islam is a load of crap, you should be put to death according to Islamic law, which is the law of the land in much of the Middle East.
And you're right. God doesn't descriminate, because he doesn't exist. But religions do descriminate - the fact that the religion was invented over the course of centuries by people doesn't make the religion they invented any less descriminatory.