In Gautham's film, Why are most of the male protagonists portrayed as a mechanical engineer?

The fact that he himself is a Mechanical Engineer could be the primary reason. Secondly there is a good chunk of Engineers as the targeted audience as well quite simply many people can relate it to their times during engineering.

Secondly he hasn't done enough movies to consider it as a pattern. He also has couple of cop movies. Couple of serial killer movies. Quite simply from a standpoint I think there could be no pattern at all really in choosing those attributes to the protagonists other than the fact he himself is one and could've chosen the protagonists to play it that way.