If you've read the New Testament, you'll know that tolerance isn't Christianity's primary message.
But the reason why some Christians may think that that torture device works as a good symbol isn't because it's seen as a symbol for torture in general (Christians don't use the cross to encourage each other go out and torture people - or at least they shouldn't), but rather because of the one specific historical event it refers to, when Christ died on a cross.
The reason why that's important is that Christ chose to die on a cross to be tortured instead of us, to take the punishment before God we deserve for our rebellion against God.
So when seen that way, the cross is a reminder of God's forgiveness of our sins. Anyway, that's one possible reason people might look at it that way.
Christianity has other symbols though. One of the early ones was a fish.