Hmmm, well I've been reading very mixed things about this movie. I can't say that Kevin Smith has really failed because a lot of people seem to like it for some reason. Personally I'm probably not going to see it to be honest.
I think the lack of a clear "message" is supposed to kind of be the point. As I understand things Kevin Smith is trying to comment on perceptions, and the way the media sways them to an extent. I think the whole thing where the movie is shot in a way that it seems like your supposd to be cheering for the evil scumbag cultists, but you really can't do it, is kind of the point. To put it in the context of Waco, people will sit there and criticize the FBI for the "botched" handling of the case, but really you can't sit there and say that they should have just walked away and let David Koresh do whatever the heck he wanted to do. In a "big picture" kind of way you have to weigh the pros and cons, of certain things, killing children is never good, but when an organization like the "Branch Davidians", or the group from "Red State" has an influance outside of what they do internally (enough to get attention) the risk of losing those children becomes the lesser evil. Shadowy orders aside, is it really better to just have the FBI walk away and let them do whatever they want to do? Not to mention the message is sends that all a whack job needs to do is keep some kids in their compound and nobody will bug them.
The inflammatory title aside, I think a big part of the issue is that a lot of people were expecting a very clear cut "conservatives are bad, liberals are good" message, and really that isn't what this movie is trying to say, it's not based around a single clear message or idealogy and is criticizing groups like the Westboro church, but also the left wing media (indirectly) and pressures, and sort of supporting a fairly right wing take on hardcore law enforcement when needed.
Of course this is all based on what I've heard, I admit I have not seen the movie, but this is what I have been able to piece together.
Honestly, I'm hardly the liberal Kevin Smith seems to be in most of his work, but it would be nice if he went back towards his older style.