He probably sees Müller as a big part of Bayern's identity.
It also would not make sense to sell him. Bayern don't need money and who out there is better or equal to Müller, who would replace him?
Apart from the Bayern identy...
Tell me who is on the market or gettable that you can get for the price and has similar quality? I do not even mean to get a player similar to Müller who is unique. No injury track record (actually never missed more than 1 club match in a row since he was 11), able to play everywhere in a front four on a very high standard, top scorer of a top 5 club in the recent 5 years and that in talent age, very consistent even if he is played not in best tactics for him, has a knock for the decisive goals against top opponents. Very experienced (5 semi finals in the CL, 3 finals in the CL, more than 60 CL matches and 60 caps)
He is not the player for 1vs1s or is an absolute individualists - but that is just important for people that do not see the other strengths he brings into the match - and that they help a team a lot just show his individual and team successes. He has really a track record that his teams win with him and loose without him.
There is nobody on the market like this - there is not many better players anyways - that is why players like him will go for big sums if they would go. There is too many money and not much top value...
But - he will not go. The club sees his value right now again on the China journey where "the crazy baby" is on tour with its Bayern. That is the market Bayern wants to get into. And the home fans and especially the media that would loose their favourite player would run riot.
And actually - people make a lot more out of the problems Müller could have with Pep than there probably are. Right now you often see them laughing together.