He deserves respect for his bat, absolutely. He is unequivocally among the very best offensive shortstops in the history of baseball. I don't believe you can question that at all.
Where I draw the line though is the over-the-top gushing that people go through over his defence. He was a mediocre defender at best. And a bad one at worst. With the exception of that time he came flying out of nowhere on the cutoff to make that shovel throw to home in the playoffs vs Oakland, basically every play on the Derek Jeter career defensive highlight reel is massively, massively overrated. The famous "flying into the stands" catch is one of my picks for the most overrated baseball highlight ever.
His defence wasn't awful enough that it should tarnish his place in history, but the ridiculous way that people throw around terms like "the perfect baseball player" or "excellent in all facets of the game" or hold up his gold gloves (and let's be realistic, he only won 6 in 19 years, and you can make a pretty good case for him not deserving a few of those) to try and make him out to be a baseball god irks me.
It is a shame that his defensive overratedness drags down his offensive prowess, but it's equally awful that the way he gets fellated by general baseball media is largely responsible for the knee-jerk way that lots of people dislike him.