Why do some people think Tom is gay?
Where did that rumor start?
Good question, but I don't know, I just follow the mob to the gallows! (Google is your friend.)
The reason he's with Katie is because she was 'bought' after Tom was caught in the sack with Rob Thomas- by Thomas' wife. Thomas' wife threatened to go to the press, she was paid off and Tom's 'staff' scrambles to find someone to make him look straight. Enter the young and gullible Katie Holmes.
I can only tell you stories I've heard. My dad was in the Navy (F-14 pilot) and some of his buddies (people I've known for 20 years) were stationed at Miramar when Top Gun was filming. They all witnessed Tom and his boy-toy and their shenanigans.
Also, for what it is worth, according to these same guys, Kelly McGillis was a big coke head at the time.