The team plays hard for Jimmy T though whether it was the depleted D line or when he was the interim coach for just one day, that's the difference, they completely quit on Harbaugh and Roman. It wasn't even the schemes, this whole season showed that nobody on offense was focused on what they have to do for a whole quarter, and all Harbaugh did was make excuses for them but behind the scenes we don't really know what he and Roman did, all we know is that they can't score, Fangio basically stopped blitzing and the D line was left on its own without Aldon Smith for the majority of the season and still ended up 7th in the league.
We can debate whether Tomsula knows his Xs and Os, but he's probably shown that he's a good enough manager of players to get his shot.
It's obvious Fangio is gone.