When villain check-raises, he's essentially saying "I have the range advantage, my raising range is polarized, and you're being forced into being the bluff-catcher."
When someone is repping a polarized range, you're generally going to be calling more often than raising, because most of your range is losing to his value hands, but beating the bluffs. To use a phrase Norman Chad once used to describe a donk bettor, "He either wants you to raise or fold, so you should call".
A similar thing happens when you face an overbet. Villain is repping such a strong/polarized range that it rarely makes sense to re-raise, because he's 'saying' he has the nuts and wants to play for stacks, but he could also be unpaired and is praying that you fold to his bluff.
If you've actually got more nut combos than villain, and can balance them appropriately (with combo draws, for example), you can 3-bet. More commonly, you have so many mid-strength hands in your range, that you need to "protect" them by also calling with some of your best hands.
You kind of have to work out which parts of villain's range will play for stacks immediately, and which combos he'll fold if you re-raise. And also consider how weak your
calling range will be (and therefore vulnerable to bluffs) if you re-raise too often.
e.g. It's a mistake to 3-bet with bottom set if villain only continues with top/middle set and a couple of combo draws. You'd make more money by calling down and losing the minimum when he has you crushed, while also allowing him to continue with bluffs. It would be very profitable, however, to raise
top set and a couple of combo draws if villain will stack middle set and bottom set (or worse). It depends on the situation of course, but calling with bottom set would usually be enough to "protect" your overpairs etc. The actual nuts can usually be re-raised every time.