I recently read an article giving the basic differences. The main one being that the air-force is generally new compared to the navy. Therefore, they don't have a lot of tradition to fall back on, so they had to create a bunch of rules and strict guidelines. The article said navy aviators get to fly and think for themselves, while the air-force guys gotta stick to the "cookbook" and they can't deviate from it. The navy aviators are encouraged to think for themselves and use they're training and personal intuition to get the job done. Go Navy!.... after i get pro rec'd that is.
This is a very cliche'd comment, that is beginning to lose relevance with time, although there is some truth to it. However, I know and work with enough Naval, Marine, and CG aviators that have flown in the USAF to have a pretty good idea of where this cliche falls apart.
From a personal side, I've made a point over the years of doing my best as a non-Naval pilot of learning how your folks "do your thing". I even tried to work a Marine Corps exchange: I would have been the selectee, but the USAF shot the exchange down late in the game. Since then, I've gotten orientation hops in a fair amount of Navy, Marine, and CG hardware, and have had the chance to see how different communities work, albeit briefly. I also work directly with the USN TPS guys on getting them in the U-2 for orientation flights each year.
Operationally, we all have stories on how "the other Service" dropped the ball, thanks to their "culture". Neither Service is perfect, and while the USAF should adopt more Navy/Marine-isms, the reverse is true too.
What's my point? I disagree with your "...encouraged to think for themselves..." comment, and the implication that I, as an AF pilot, do not. You could not be more wrong. That's ok: we all need time to learn and grow. I'm guessing you are quite new to military aviation.
When you've got the background and experience of seeing USAF ops, and when you have plenty of close friends with 6-9+ years as USAF pilots, then maybe you will have a clearer picture. Until then, keep an open mind, and learn all you can about all the Services.