I don't believe that the audience would have any trouble with a gay captain or an alien captain. It's the people who wouldn't be in the audience, either out of homophobia on one hand, or a lack of ability to identify with the alien main character on the other, that are the problem.
That's some pretty convoluted logic.

The "missing" people
are in the audience, for the purposes of discussion. If we assume that they're not part of the potential audience, then why even discuss them?
Face it, your thread is inadvertently revealing just how narrow minded Trek fans are, even ones who are dedicated enough to seek out a place like this one. I find it slightly astonishing but for that, I blame myself, for being insufficiently cynical. Not being able to identify with a character with blue skin or pointy ears comes from the same source as not being able to identify with a character due to their having other 'alien' qualities such as the 'wrong' gender, race or sexual orientation.
My hunch is that an alien captain (who is a straight white male American in all but the surface attributes) would be far more acceptable to the "audience" (defined as anyone who might watch Trek if it catered sufficiently to their prejudices) than a gay male captain who is otherwise perfectly "ordinary" (white male American). Some oddball makeup is going to be a lot less threatening than dialogue that reveals that Our Hero likes guys.

How can cosmetics be more threatening than sex?
How many other countries is it considered illegal to be homosexual? Women were never locked up because of their gender.
Wow, I guess you're unfamiliar with such lovely places as Saudi Arabia, Iran, Sudan and Afghanistan. Lucky you. And not to pick on the Muslims, there are plenty of non-Muslim nations where women are subject to downright terroristic methods of oppression as well.
No. I do not understand this obsession for gay people in Star Trek. Besides, there has already been a gay actor in Star Trek.
More than one, I assure you.
The only real obstacle to a gay character (other than bigoted so-called fans, of which there are many, judging from the responses to threads that broach the topic of a gay character) is that by the 23rd C, homosexuality should be so trivial, that it would make as much sense to have a character who is defined by hair color.