I think the Willie Horton ad was the big thing that did him in.
I know that that is a popular theory, but I think Dukakis was doomed to lose. He just wasn't a very good candidate.
1) Little charisma (not that GHWB was a Clinton-like charmer)
2) On the opposite side of most Reagan/Blue Collar/Ethnic Democrats (whichever term you want to use) on most issues
3) A guy who ran on "competence" and on the "Massachusetts Miracle"... but yet as the campaign was in mid-stream the Massachusetts economy was tanking.
4) He wasn't even that popular of a politician within his own Democrat heavy (and at that time, even MORE Democrat heavy) state and certainly didn't have the kind of appeal to win Sun Belt or Rust Belt voters
Willie Horton, the tank, the Bernie Shaw question about Kitty's rape and murder all had some part, but I bet that after each one of those events he was STILL in the lead. The problem was, imho, that voters just didn't know him well, and when they found out more about him they didn't like him.
It might be tempting to blame that on Lee Atwater's dirty tricks, but maybe the guy just wasn't a very good candidate. I can say from experience of living in Mass (and working at the statehouse as a college intern during some of his years... not that that gives me much expertise) that he wasn't really that good of a governor either.