One of the things it took me quite awhile to realize was that RAW often didn't believe half the stuff he wrote. Often he was more interested in the mind set of the believers than the belief.
Also, sometimes I think he just intentionally fucked with his readers.
He also said some shit that was completely wrong, and probably not on purpose (his statements about feminism come to mind specifically here -- if he understood mainline feminism he would probably count himself as an adherent of it).
In some cases, it's difficult to tell whether he was legitimately wrong or if he was trying to fuck with people, but it doesn't much matter in situations where people cite him as an authority on things where what he wrote was very warped (his descriptions of QM and of information theory come to mind here).
There are also notable instances of what seem to be running feuds. While so far as I can tell his annoyance at James Randi is justified, Carl Sagan often comes off as being primarily in agreement with RAW, and RAW ascribes to him some ideas that in retrospect don't seem to be his -- so RAW's statements about Sagan just generally shouldn't be trusted.