I don't hate squeezing with 99 (i think it's probably profitable with ATC), but I rather do it with my lower pairs 22-55 (or perhaps 66), so you don't get into situations like this.

Also if I bet the flop I'd make it higher, because by betting you're already committing anyway and we'd want the guy to fold. Problem is by squeezing and c-betting you've committed to this pot and we can't be too happy about getting it in