The biggest factor in Florida is that the ballot marking system that Florida used at that time was extremely prone to failure, especially with regards to machine reading of ballots (which itself could cause an apparent mark on the ballot!). This means that trying to divine whether or not a ballot recorded an intent to vote for a candidate can be subjective and depends on the exact standard you want to use, which Florida didn't specify (and the Florida Supreme Court ruled was ultimately too vague).

Since 2000, most states have switched to optical scan ballots as their paper records. These ballots have much lower error rates, closer to 1 error per million votes. I don't think there's been a single race using optical scan ballots where a recount actually caused a winner to switch.