In my experience non compliance with SOPs usually stems from 2 primary areas.
1. The SOP is deemed not to be applicable. This can sometimes be valid, but has a general tendancy to become habit forming, not only in regards to that specific SOP (repeated it often enough and the pilot convinces themself that the way they do it is the way its supposed to be done!) but also more generally, as in 'SOPs are there for my guidance'.
Ultimately SOPs can not cover all circumstance and should be our servants not our masters, but if you are discarding them willy nilly then you are in danger of going past the occaisional excercising of good judgement into the territory of blind arrogance.
2. The SOP is unworkable. As in so completely unuseable that to attempt to do so would be immediately dangerous. In this case even the most disciplined pro-SOP pilot will decline to comply!
In my experience, 99.9% of deviations come in the former category and only cary a very small risk one way or the other (i.e. compliance may not always have been safer).
Very occaisionally the second category, usually followed by the procession of people heading for the chief pilot's door muttering 'what the !??!', followed by an SOP change. But in the intermediate period a lot of arguements and risk on the flight deck.