SPOILER! Kattints ide a szöveg elolvasásához! Hulk IS Banner. Loki REQUIRES touching people with his staff to control them. Banner touched the staff. It doesn't matter if Hulk is or is not resistant to mind control, Banner is not resistant.
All Loki needs to do is invoke the change UNCONTROLLABLY. Hulk is Banner's id (not I. D., look it up if you need to). Literally.
When Banner controls the transformation, like in TIH at the end when he 'aims it', he has some level of consciousness while converted. When the transformation occurs without his consent, he is fighting it, and still in that 'state' during full-on Hulk mode.
Basically, Helicarrier = Mindless Hulk, not mind-controlled Hulk. Manhattan = Professor Hulk.
Again, Banner's state during transformation determines the end result. This is in the comics, he CAN control it in the movie anytime he wants, and when he does, he controls the Hulk. But also, it can come out without his control, and the Hulk will mirror that. It still feeds on his emotions. When he is enraged, it is enraged. When he is harnessed, and so on and so forth.