Why do some gyms have rules against being shirtless? How exactly is it offensive, uncomfortable or intimidating to anyone?

It's not unless people let it be. E.g., the intimidation factor is bogus; you can see a good body thru clothing, and many of the best built are the nicest mentors anyway. As for offensive, there's indeed a current prejudice against upper-body nudism that's burgeoned since I was young.

The only good reason is to protect the upholstery from getting perspired on, and that's better solved by requiring wipe-down towels; it's easy for some people to sweat right thru a tee. And if they let the females go sleeveless or even bare-shouldered and -midriffed ...

As already mentioned if you have no shirt on your gonna get more sweat on the equipment and nobody wants to use a sweaty piece of equipment. People will judge and compare themselves to others and those out of shape or really skinny will feel intimidated by those in good shape and the sight of a sweaty body even one that looks aesthetically good will still gross some people out. If you don't want to wear a t-shirt because you find it restricting why not wear a vest instead?

Depends if your a girl then it'd distract all the guys.

Lol... On a serious note, some people find it distracting seeing muscular shirtless people when they want to look like it too and so discourages them.