Exactly. For instance: with meager fortitude you are less tough than you ought to be. This is the flaw of your character. It would be silly if a character's fortitude would increase with class abilities. (Your saves still increase like they normally would, just not with class abilities.)
The minus is supposed to hurt, that's why it is a flaw. If the flaw doesn't hurt your character anymore at 3rd or 4th level it really isn't a flaw, even though the benefits of the feats still apply.
The minus is supposed to hurt, that's why it is a flaw. If the flaw doesn't hurt your character anymore at 3rd or 4th level it really isn't a flaw, even though the benefits of the feats still apply.