Captive and Mech, Incognito is a very physical dude who can be dirty at times. The thing is, he plays as dirty as the league lets him, and I don't think he's trying to hurt anyone, just slow them down as effectively as he can legally. In other words, he's an offensive lineman in the NFL. He has moments that are pretty insane like the leg biting but otherwise he's just a typical brawler in the trenches.
No idea why the ref didn't throw a flag on that play but at the end of the day Smith swung a helmet at the dude's head when he had presumably done nothing illegal. The two guys just hate each other and it manifested in that play, but the helmet swinging crosses the line. That was clearly beyond playing football, he was trying to hurt Incognito out of frustration.
Mech, you can whine all you want about a coach standing up for his players but how can you expect anything less? If any coach saw a player do something like that to one of his linemen I'd imagine he'd handle it the same way Philbin did.