First, a big reason you didn't mention is that Nader running as a third party syphoned votes primarily from Gore.
Second, the butterfly ballots are a bad design. If you were to design a software interface in the same way and with the same failure modes as a butterfly ballot then you can't blame the user for not understanding it. Those ballots were not designed with usabilty in mind - calling people who failed to use them properly 'illiterate' is placing the blame in the wrong place.
Third, a plausable implication from your above comment is that you believe that people who didn't vote for the candidate you prefer are somehow less intelligent than you. I'm not saying that was your intent, but I can see how somebody might draw that conclusion from your comment.
Technically, it's incredibly easy to "say" whether any one factor had nothing to do with the outcome - in fact, this seems to be the overwhelmingly normal behavior of individuals, the media, and government officials.
What's impossible is to know whether any one factor had nothing to do with the outcome. More interestingly, it also seems nigh impossible for people on either side of the dispute to simply acknowledge that great certainty exists everywhere within the complexity of life, that we simply do not know what has taken place in this situation, or in the thousands of others that people argue about, with many of these arguments having a lifespan of decades if not longer.
It may seem like a trite idea, but I believe that if we could have more widespread realization and acceptance of this fundamental truth, perhaps we could move beyond this increasingly deep rut of partisan bickering we seem to find ourselves in.
It was clear this was going to be a problem after the 2000 Presidential election came down to a few semi-literate Floridians. One definition of "chaos" is a system involving large numbers with sensitive dependence on very small margins, and that's what we have here.
Edit: Well, I guess we're still hearing from the semi-literate Floridians. What are the high schools teaching kids about that election, anyway?