I still think him taking the part was some kind of very bad inside joke. He's been publicly denying his homosexuality for years and it's been rumored that's the reason he chose to join Scientology in the first place. Like many self-hating gays, he's chosen to make a joke about it... "See? if I was gay like you all have been saying for years, I couldn't take the part..." Is he really gay but using the openly homophobic stance of his Church to hide it? Most certainly.
It is a fact however that Scientology is promoting homophobia and self hatred and as one of the few remaining openly declared Scientologist and standard bearer, he helps promote it. Someone said that some Christians being homophobic doesn't mean ALL Christians were. That's very true but there are no "lapse Scientologists" and Travolta has defended the cult's wacky ideas many times over.
I don't care for him as an actor or a person but that won't stop me from seeing this movie. I doubt a movie with a story like Haispray is likely to end up promoting homophobia, whoever plays in it.
I do think however it's a good thing that someone used the occasion to publicize the fact that Scientology and people like Travolta are homophobic de facto.
"What book of rules says that theatre exists only within some ugly buildings crowded into one square-mile of New York City? Wherever there's magic and make-believe and an audience, there's theatre..."