There's two reasons for this, one there is a difference between religion and fundamentalism, and two, I don't necessarily have a problem with general, but I definitely have a problem with fundamentalism.
Yes, there is a difference between religion and fundamentalism. Both often go together, but they don't necessarily have to be one and the same. First, I'll define the two, in my own way. Religion typically involves a belief in a deity or deities and a holy text. Often there is a prophet who followers of the religion see as the messenger of the deity, or as a deity himself. Depending on what the religion teaches, that in and of itself is not necessarily a bad thing, though more often that not, because of the religion's teachings, and/or the actions of it's followers, it becomes destructive.
Religion in and of itself, though I disagree with it, I often have no problems with it, but when belief in a religion becomes a form of fundamentalism, that's when I have a problem. Fundamentalism is the combination of ignorance and intolerance with religion. Fundamentalism in religion is the most common among those who believe that their faith and holy text are infallible (without error), and believe that their faith is the only way to achieve a positive outcome in the afterlife (all those who don't believe, regardless of how morally they lived their life).
Fundamentalism is deliberately isolating yourself from the outside world, because you feel it is too evil, and rejecting anyone as evil because they don't look, act, think, or worship the same deity as you (or refuse to believe in one at all), and forcing your children to do the same, and making it much harder for them to function when they become adults. Fundamentalism is feeling that you and your congregation are more morally superior to others, and putting on a veneer of holiness, when in reality you are no better than everyone else, or are using your act of self-righteous to cover up horrible evil done by yourself or your leaders. Check out my archive of posts on the IFB movement to see what can happen when a group isolates them themselves, and puts on an act of holiness like that.
Fundamentalism is also believing that you have the right to use the force of law or social pressure to force others to live the same way that you do, and to persecute those who don't look, act or think you do, which happens on a daily basis in the US.
That is what I reject, and despise, not religion itself. I admire those people who still believe in a faith, but are open minded people, and reject fundamentalism. People who believe in loving others, no matter who they are. Some great examples are liberal Christians, I like reading bloggers like John Shore, or Lewis of the anti-fundamentalism blog, Commandments of Men. I enjoy seeing people like St. Louis minister Larry Rice, who has made it the sole mission of his church to help the desperately poor and homeless of the city of St. Louis, and has clashed repeatedly with city government over the treatment of the homeless by the police department of St. Louis.
I also admire Wiccans, all of the Wiccans I have ever encountered in person or online have been very open minded people, one of good friends is a Wiccan, and when I first met her (I met her when I was in the process of getting out of fundamentalism), I was surprised at how she lived out a live of loving and accepting others, more so than the Christians surrounding me who are supposed to be followers of Jesus, who told people to love others as yourself.
See, I don't hate religion, though my rants may lead you to think that sometimes, my real issue is fundamentalism...