You're right. That semi final loss was hard to take, so it's understandable why they were critical. I was talking about this very moment though.
It was for a lot of people, even though some of the contributors to the result were out of Pep's control. He did make some tactical errors too but we've had set piece problems for a while (look at the Munich CL final). And the players made that fatal mistake of letting down in the league and getting complacent. Even before that match, everything was slowly getting worse. After I think 19 straight wins, we had that one loss to Augsburg that was just the catalyst to everything going wrong.
Also, no matter what, even now, he will get comparison to Jupp Heynckes, who will always be remembered for the treble even after so many people lost faith in him after losing everything in the 11-12 season. When Pep signed for the club, Bayern were still underachieving and no one expected the season to go as it did. It was just unfortunate for Pep, I guess.