This answer is more speculative than I'd like it to be, so if someone answers with more references I can delete this. Anyway, it seems to me like there are a few explanations for this:
1 - The Naboo pilots were inexperienced It seems to me like the Naboo Royal Space Fighter Corps wasn't really designed or trained for large-scale warfare. Naboo fell almost immediately to the Trade Federation, and until the Clone Wars it seems like the Republic didn't have or need a standing army, so based on this evidence it seems like Naboo's pilots were never expected to take on capital ships. Thus, a tactic like 'fly through the hangar to the reactor and blow it up from the inside' just never occurred to them, because they've never actually fought a ship that had a hangar.
2 - The hangar isn't always open. I'd guess that most of the time, the ship's shields are going to be covering the hangar, preventing ships from entering and/or leaving. So maybe Anakin just got lucky and flew through just as a droid ship was entering/leaving, and the other pilots didn't think they'd have a chance of pulling that off intentionally.
3 - No one knew what the inside of the ship looked like. Like I said, Naboo fell almost immediately to the Trade Federation, and it seems like no one was prepared for the invasion. So there's a good chance that the pilots involved in the battle were seeing the droid control ship for the first time. And while they might've been able to detect critical systems from their outside view, they'd have no way of seeing the inside of the ship until they actually got inside. For all they knew they'd fly right into a wall milliseconds after entering the hangar (and really, who would design a ship that lets the enemy fly straight through to the reactor?).
From all of this, it seems to me like the other pilots were defaulting to "shoot the outside, hopefully we can break through the shields eventually" while Anakin happened to accidentally do a bunch of things that should have killed him but ended up working in his favor. Kinda like pretty much everything Jar-jar did in the ground battle.