For me, complete tolerance and my personal morals are at odds with each other. Under full tolerance, there can still be judgment, but you cannot act upon that judgment; hate crime will not be fought, bullshit theories will not be debunked into oblivion, etc.
You need to be careful with the word "tolerance" though. It sounds like a magnanimous thing, but it still lets you keep your self-inflicted moral or logical superiority, arrogantly placing yourself at a higher level than the other. For instance, if I, heathen, would ever say I "tolerate" Christians, you can kick me. People believe different things, that's a given, saying you "tolerate" that doesn't paint a pretty picture of yourself. Better to just be neutral about it, until it clashes with your morals.
A final remark: a lot of so called "tolerance" is just indifference, and should be called that.
End of ramble.
Yes, in many cases indifference would be a better word, and judgment calls still do need to be made.