Cher Robert,
Two points on this question:
1. It was, as our friends point out, essentially a 'domestic uprising'
2. Napoleon did not want to use first-line French troops for what was a secondary theatre in this war (he was clearly focused on the main strategic challenge: the Austrian Hauptarmee). That is not to denigrate in any way the performance of the Bavarians in 1809 (it was generally competent and sometimes superb). However, if Napoleon had to dedicate rare combat assets to a secondary problem, he would turn first to his Rheinbund allies rather than French units. Especially in this 'Bavarian internal' problem.

Two additional (by the way) thoughts:
A. Note how Napoleon withdraws even the Bavarian regulars when he needs regular troops in the Danube valley. He is willing to tolerate and contain the disturbance in the Tyrol (annoying, but not vital) to concentrate assets for the true strategic aim (defeat Charles and the Hauptarmee).
B. Napoleon did use French second line troops (march battalions, new fourth battalions, provisional dragoon regiments, isolées, etc) to supplement the Bavarians and other German troops who were contending with rebellion in and raids from the Tyrol (and the Vorarlberg). German second-line troops (especially Bavarian), also played a key role (and Rouyer's Thuringians are added later).
Similar combinations, their image boosted by active deception campaigns, were the mainstay of all his 'rear area' operations that year.