Hummels started 25 games in the Bundesliga last year and was only an unused substitute for half-a-dozen matches, yet he remained on the bench for Kovac's first league game in charge last month when Bayern beat Hoffenheim 3-1.
Niklas Sule and Jerome Boateng started on that occasion, with the former reverting back to the bench when Hummels came in for the 3-0 victory over Stuttgart the following week.
Despite being an established figure in Bayern's team since joining from Borussia Dortmund in 2016, Hummels understands Kovac will need to alter his defensive options, particularly with two games most weeks for the next few months.
"I hope he keeps the rotation all season long," Hummels said in an interview with Welt am Sonntag.
"There will always be players injured or suspended. We have almost until the winter now only 'English weeks'. Therefore we need the big and qualitative squad and the rotation."
Hummels did not stop to speak to the press after the Hoffenheim game, yet he denied that was anything to do with Kovac leaving him out of the team.
"That does not mean that I did not accept the coach's decision," he added.
"If I did not accept them for the enormous quality of our central defence, I would not have a sound self-assessment."