Obviously the plot sequence demanded that they not simply shoot him down, but it was weak, I agree.
Plus, (it's been awhile but anyone with the DVD handy can check) apparently if you watch the scene right before it you can clearly see they have plenty of rockets left, so whoever was modelling that scene forgot to at least give the appearance that what the pilot said was reasonable! gaffe).
I once thought perhaps Dooku mind tricked the pilot to just give fake information to the Jedi onboard. That would mean they were incredibly gullible though, but who knows!
I take it he was referring to some game experience. Though I'd point out that the games always play fast and loose with the mechanics of Star Wars tech, for the sake of balance and gameplay, so the games aren't a very reliable guide for how the movie stuff is supposed to work.