Hmm, you know, I can see John as a control freak now that you brought it up, but I never really saw it in canon! I get some control issues from him, but I think of it more as a response to trauma than a core character element - he tries to keep control of the little unimportant things because he knows he can't control the big ones. (Though I have to admit I'm with Kate in having trouble with Dom!John - I don't necessarily read him as sub, and I can see some versions of him domming if that's how a particular relationship worked out, but I really don't see it as an overriding preference for him.)

Also I would never, never think of flying as fundamentally a control thing, but possibly that's because flying for me defaults to WWI-era technology where it is definitely not all about the pilot's skill!