You are talking about wealth and prestige that were accomplished over decades. Of course it just won't happen over a year or two that Bayern lose that position of supreme reign over the Bundesliga, especially now, since they are not only the best in Germany any longer, but even the best in Europe (=world).
Still BVB has managed to win the League two years in a row and is still fighting back just now, despite losing their best/2nd best (depending on how you rate Reus) player to them. It's no coincidence that they are having the best starting record into a season of club history just now. Their only problem is that Bayern is even stronger. But how can you blame the likes of Dortmund or Leverkusen for that, or any team for that matter.
If the Bayern of the Jupp/Pep era were playing in England, Spain or Italy instead of Germany, they would still top those leagues and you would make the same comment about the respective league, instead of the Bundesliga.
Dortmund are really, really good as their performance last season had proved especially in the CL, as their two clashes with the current EPL's best have proved. If Dortmund were playing in the EPL or La Liga, they would most likely still rank among the 3 best teams respectively. Again, their only problem is that Bayern are experiencing an era of supreme excellency. With a Bayern of the mid-00's instead of Jupp/Pep's Bayern, the Bundesliga would have already seen a change of the guards with Dortmund taking the seat at the nation's helm.
But Bayern is run by very smart people (compared to many other big clubs or national upcomers) and a state of long-term decay, as was experienced by Gladbach for instance, simply never happened with Bayern, since Bayern's leadership always managed to fully capitalize on the club's wealth and prestige.