Because he came out against gay marriage:

“Your invitation to Reverend Rick Warren to deliver the invocation at your inauguration is a genuine blow to LGBT Americans,” the president of Human Rights Campaign, Joe Solomonese, wrote Obama Wednesday. “[W]e feel a deep level of disrespect when one of architects and promoters of an anti-gay agenda is given the prominence and the pulpit of your historic nomination.”
The rapid, angry reaction from a range of gay activists comes as the gay rights movement looks for an opportunity to flex its political muscle. Last summer gay groups complained, but were rebuffed by Obama, when an “ex-gay” singer led Obama’s rallies in South Carolina. And many were shocked last month when voters approved the California ban.

Evidently, they don’t care that he supports civil unions. It’s all or nothing I guess. I think they’re making a mistake here, they’re trying to make Obama choose between Evangelicals and gays, they lost that battle the last time:

The rapid, angry reaction from a range of gay activists comes as the gay rights movement looks for an opportunity to flex its political muscle. Last summer gay groups complained, but were rebuffed by Obama, when an “ex-gay” singer led Obama’s rallies in South Carolina. And many were shocked last month when voters approved the California ban.

If they flex their muscle and he doesn’t respond, doesn’t that make them look weak? Doesn’t make sense to press an issue unless you know you can win. I think hitting against such a benign pastor (he is certainly not a member of the religious right), is a tactile mistake. Warren is certainly no Dobson or Robertson!