Well I've never heard of the Phantom Menace trailer thing specifically being related to the Wing Commander movie, but I definitely have heard of people who buy tickets for some random movies just to see the Star Wars trailer at that time.
FOX did, indeed, attach the trailer to Wing Commander hoping that it would attract more interest to WC... but Lucasfilm complained and FOX ultimately put out a statement that the trailer could be attached to any movie coming out that week. They didn't actually change their instructions to theaters, though, so most everywhere Phantom Menace stayed with Wing Commander.
(And why do I know this crazy thing? Chris Roberts actually forwarded several fan sites his e-mail conversation with a FOX rep explaining that they put out the statement to satisfy George Lucas and that the trailer would still be with Wing Commander regardless, hoping we would unofficially let people know what was going on.)
I went to see it twice in the theater, I never saw that. I find it very hard to believe people would pay $10 to go see a 2 minute preview and then walk out when they could JUST DOWNLOAD IT ONLINE!
Yeah--you can say it was before everyone had internet access... but I bet that as a group, insane Star Wars fans with money to burn were fairly well connected in 1999.

Actually, I remember the various Phantom Menace teasers being the first internet video that I could just click on and watch...
Movies didn't cost $10 in 1999, though.
(I think I saw Wing Commander in theaters five times... one of those was the Austin premiere, which was a pretty incredible experience. The others were Chris Reid and I trying to note down all the little details like the ship names from that one screen because we knew it'd be months or years before we could get it on home video.)