Before you posted the outcome I was going to make the case for the check-raise.
[To be fair, I do mostly lead out there too, probably a bit less than 1/2 pot for all the reasons Steve et al mentioned - but moreso if I"ve already been seen to open post-flop a decent chunk of the time.]
There are plenty of legitimate pf raising hands that miss this flop completely - stating the obvious, holdings like AK, AQ, maybe AT, any pocket underpair to the jack plus any creative raises if your read isn"t quite right. If your oppo is in an ABC mood he"ll get out of the way to any respectable lead, as happened.
IMO people worry too much about flopped bare flush draws against a single opponent. The chances of villain holding two clubs (now that we know that two of them are out there on the flop) are less than 5%. Factor in the chances of then actually hitting the flush on the turn even if he does have clubs in the hole and you"re looking at 1 in 100. If we can safely rule out the up & down draw (and it doesn"t sound like you put him on 67/63/32) then his only draws are to the overset (5%) or to one or two pair, which is clearly a result for us.
He could scupper our check-raise by checking behind, but any overpair to the jack, the jack itself PLUS most of the hands I was saying he"d fold if you lead (why wouldn"t he think his AK/AQ/TT-66 is ahead here?) should probably result in a c-bet on the flop for us to re-pop.
So I accept it"s slightly higher variance, but I do think there is some merit to checking the flop to either (a) hoover up any light c-bet and/or (b) let him catch up a bit to improve our return on later streets.