In the book "Freakonomics,when Steven Levitt says he's not good at math does he mean it?

It appears that he means it to some extent, but is to some extent being self-deprecating.

Levitt entered graduate school at a time when the amount of math required for admission to a top economics department was less than it is now.  (See the Freakanomics blog link below.)  He apparently had only one calculus course in college, which is not much math at all.

Now, the career he has had after graduate school shows that he is at least competent at higher math.  For example, follow the uchicago link below and start reading from p. 646 (or look at the appendix p.656).  It's clear that the man isn't exactly struggling with math.