It is obvious that Bayern Munich dominates in a number of areas including reputation financial resources and infrastructure. The Bundesliga championship however measures actual strength on the pitch which goes beyond having a roster full of illustrious players. Numerous variables must come together for a team to be the strongest over the course of the full season not just for a single game or month. The game mental component and any potential complacency that results from ongoing success can have a big impact. It is usual for a team used to winning to mistakenly let its guard down giving hungry and tenacious teams a chance. Such events occurred during this Bundesliga season but ultimately everyone saw the expected conclusion.
I already said this before, but i really think that the chances of Borussia Dortmund to become Bundesliga champions this year were extremely high and i don't think that they will get such a big chance again in the next 5 years or so. As you already said, Bayern Munich is by far the strongest team of the Bundesliga and if they are able to at least reach like 85% of their maximum performance level, then they will win the Bundesliga no matter what the other clubs are doing. This year this was not the case and still Dortmund was not able to profit from that. Now Bayern should be alarmed again and take the next season more serious.