I understand his reasoning perfectly. I don't understand your reasoning though...
His reasoning was:
you limped in preflop from MP, which means you're probably a weak, passive fish and he wants to isolate you by raising and taking the betting initiative. He has a suited connector (a speculative hand), which plays very well against fishy calling stations that tend to stack off with top pair 100% of the time. In other words, he has good implied odds
to play a hand like 43dd.
This is a perfect flop to Cbet because most of your range is going to miss this flop, so there is a lot of fold equity for his bluff.
He now picks up a combo draw (OESD + flush draw), so it makes perfect sense to barrel here and try to get you to fold hands like 44-99 and maybe even some weak Tx hands. Once he gets raised on the turn, he only needs 30% equity to make a break-even call. Given that his combo draw has more than 30% equity against a hand like QQ, it makes sense for him to call it off here.
I think that the villain played perfectly.