When I was a phd student, I often felt that my PI did not contribute anything.
Now that I advise students myself, I see how much effort it takes to get a project of the ground. I have an idea, write a grant application, administrate the project, hire students, steer them in the right direction. When a student joins the project, I have potentially invested many years of work that might not be visible to a student.
For example, I might think that a certain class of materials might have some property. Later I get a student and have him synthesize the materials. Even if I would not talk to him during his entire experiment, I have still made a substantial intellectual contribution.
From the students point of view it will look totally different. He'll probably think that he designed the molecule all by himself. I try to stay in the background, but that doesn't mean I don't contribute intellectually.
That doesn't mean that your PI contributed something to your current paper, but he might have done so in the background. If your PI feels deceived, rightfully or not, he can make your life miserable.
I don't know the exact circumstances of your situation, but in either case, you should just move on. Nothing you can do about it that won't backfire badly. Having your paper listed in his application really doesn't create any disadvantage to you, and I don't think your PI has done anything wrong or unethical.
Also, maybe he would have liked to contribute more, but he is busy getting money so that his group can continue.
Tricky situation, maybe next time you can nudge him to contribute a bit more by more forcefully including him in the discussions. Then you will not have to worry and can add him as an author in good faith, and your PI will also be happy because he gets to spend some time away from writing grant applications.