Fielding percentage is a virtually worthless stat. It's good at measuring what it measures, how often someone makes an error. But I think anyone who has every watched much baseball would realize that there is much, much more to defense than just not making errors, primarily range.
UZR is not a perfect stat, but I think it's fairly reliable. Every other fielding stat (Win Shares, Range Factor, Zone Rating, etc.) comes to a similar conclusion about Jeter's defense. Plus, I think it is generally accepted that while he has a good arm and goes back on popups well, he has lousy range.
I don't think based on UZR we can definitevely say that Jeter is the worst SS in baseball. But, based on all the available evidence, I think it is valid to conclude that Jeter is somewhere between below average and the worst SS. Where in that range he falls is up for debate, but I don't see any basis for a conclusion outside of that range.