It seems pretty clear that when Brady talks about 'hitting the open guy', there's more to it than just scanning the field after the snap and instantly seeing an open receiver.
Each play is designed to get a favorable coverage matchup versus a particular defense. Armed with this knowledge, he can scan the defense at the line before the snap and get an initial idea where his best likely option will be.
There's probably another read right after the snap; did they actually play the defense he expected, or did they switch out of it? In either case, these reads add up to a preferred receiver, or maybe 2. These are where TB looks first. You can see this on most pass plays - his eyes immediately go to an area of the field where he expects to throw the ball.
Then comes a decision - throw it there or not? This is often based on the matchup, and not the appearance of the receiver suddenly being 'open'. For example, I remember 2 separate passes to Welker in 2007 where TB anticipated that WW would beat his man deep, and he threw the ball before WW had even drawn even with the defender. Same thing with Moss. If TB reads one-on-one with Cromartie and he feels that Moss has a huge advantage in that matchup, he's probably going to throw the ball there even if Moss isn't technically 'open' as the pass is thrown. But if Moss is running a deep route and Cromartie is giving a 10 yard cushion, maybe TB goes on to the next guy in the progression.
And yeah, there are passes where TB has a receiver in mind, but doesn't look at him immediately, trying to look off a defender. I realize that. But most passes seem to be based heavily on the early reads and the projected best matchup. If someone on the opposite side of the field breaks open because of a defensive lapse, it's certainly possible that he might be missed in some cases. I'm guessing that's what happened a few times last week. And, frankly, Cromartie played pretty good D on Moss, unexpectedly. It happens.