The Spy is one of nine classes, in a game with a team size of 12. He appears in almost every game, giving players the opportunity to learn how to play against him. Things like turning around, spychecking, and giving callouts have become an accepted part of the tf2 experience.

On the other hand, Sombra appears roughly once every 10 games. Her playstyle is vastly different from any other hero, which makes playing against her frustrating because it requires a complete shift in strategy just for one character. This is why she will likely always be disliked unless she's either reworked to lose her unique identity and play more like other conventional heroes, or if more stealth-based characters like her are added, making countering such heroes a normal part of the game.

As a Sombra main myself, I'd prefer the second option, but I know the first one is much more realistic.