I think you have two issues here. Respect, and tolerance. You can respect someone and still not show tolerance for what they do. Enemies and people with conflicting opinions can respect each other. Often times their goals are something you can relate with, and so you can respect them, but the way they go about trying to reach their goal is often something you do not agree with.

For example terrorists. You might agree with a terrorists goal, and respect them, if say they just want to bring political change and stop the invasion of their country. The goal is reasonable, and it is something you can understand and relate to. However they go about it by blowing people up. That is something that should not be tolerated and it isn't acceptable. So the means by which they are trying to accomplish their goal is bad.

Usually the more extreme the method is, the harder it is to agree with the persons goal, because it is colored by the horrible things they are doing to try to reach it. If a person is being an idiot you can respect that the person means well, but still think their methods are moronic and harmful. If it is harmful to just them self then you should respect their choice and let them harm them self. If their choice is harmful to others, then you have a right to try and stop them from harming people around you.

Lastly we are all humans, and if nothing else we should be able to respect each other because of that. No matter how bad someone is, you should always have some level of respect that they are a human. There are some things, that no human should be put through. Things like torture. If a person if harming others we should stop them from harming others. Not because they need to be punished or because we hate them, but because we had to in order to protect our self.