He's proven himself to Pep after he doubted him already. It looked like Pep wouldn't make much use of him, but changed his mind after a few goals/good performances. Now, he's part of the system.
When did Pep doubted Mandzukic and to whom did it looked like he wouldn't use him? Until now Mandzukic started 5 liga games and was used as a substitute in the other one(no other player except Neuer started all 6 of them), started in the german supercup, started in the european supercup and started one of the 2 cup games(in the last one he was rested and Pizzaro played instead). So if Pep doubted Mandzukic, I can't imagine what he thinks about his other players.
They had too many dressing room brawls already with Jupp Heynckes being the only one to bring some balance and harmony. Pep doesn't fare as well as him in that matter, seeing he brought in Thiago (whom some of the Bayern press call his teacher's pet)
What other journalist except Honigstein called Thiago his teacher's pet(a journalist who wrote after 2 games that the players doubted Pep when is clear just how good of a relationship Pep has with them, especially with the ones that matter the most: Lahm, Ribery or Schweinsteiger)? And a cule should know by now that Pep doesn't favour anyone who isn't Messi..and if he benched Ibra for Bojan, I'm sure that he won't have any problem in benching Thiago(especially when Kroos is in the best form of his life and he has improved in defense).
and benched Mandzukic too much in his first games, which he changed soon after. Mandzukic will definitely get his playing time.
Like I said, Mandzukic has been benched twice: in the 6th game of the season(3 days before Bayern met Chelsea) and in the 11th game of the season(against Hannover, at home).
And here's what he had to say a few days ago:
"
Pep Guardiola is vigorously rotating his squad, but he almost always starts with you. You’ve only started on the bench once, in Freiburg.
I'm delighted the coach is putting so much faith in me. I try everything I can to repay that faith. I'm really enjoying it again this season, and I have no problem with two games a week. It's easy for me because I have lots of energy.
You've scored in each of the last three matches, and you're top scorer at the club again with five goals in total. Would you say you're on track?
I had a good pre-season. My target is to be even better this season than last. I'm in very good shape again at the moment, but not in absolutely peak form in terms of rhythm. I'll get even better.
How's it going under Pep Guardiola?
It's very good. His tactical ideas are terrific, he wants the ball, he's fantastic when he talks to individuals, and he’s always game for a laugh. It's working out.
You're exceptionally strong in the air. Is that something you were born with?
(laughs) Maybe. My father was a centre-back and superb with his head. But it's primarily the result of training. Even when I was small, I worked a lot on heading. Nowadays, I often stay out on the field after training and ask my team–mates to send over a few crosses.
It's all practice, practice, practice."
It's hard to think that Pep wouldn't like a player like that.