Pams House Blend has a number of articles on this.

When you look at the advice he gave the Kerry in 2004 (from Politico):

A version of this story is already in print. In 2004, Newsweek reported, without a named source, that Bill Clinton had suggested Kerry “to back local bans on gay marriage.”

Shrum has more, and different, detail:

…”Kerry, Clinton ventured, should consider defying Democratic interest groups by endorsing the Bush proposal for a federal constitutional amendment banning gay marriage.” Shrum reports that “this was a flip-flop too far for Kerry.”

You also have a report from Newsweek in 2004:

Clinton Advice Spurned. Looking for a way to pick up swing voters in the Red States, former President Bill Clinton, in a phone call with Kerry, urged the Senator to back local bans on gay marriage. Kerry respectfully listened, then told his aides, “I’m not going to ever do that.”

You also have his spinelessness on the Military’s Don’t Ask, Don’t Tell.

And you have him actively campaigning in the back rooms in 2004 against Howard Dean, because he felt that Dr. Dean’s signature of civil unions in VT would “kill his campaign”.

I don’t think that this from a Sistah Soljah type sense of politics, but rather from a deep seated discomfort with gays.