Because practically, aren't ideas tied to people? I don't think you can have an idea survive without people keeping it alive. So how do you express intolerance for "bad" ideas without letting that expression bleed into an intolerance for the people propagating the "bad" idea?
Take a certain popular religion, for instance. This religion can be judged as evil if you are secular or pro-reason (as opposed to faith). But individuals who practice this religion do so as individuals, and may place more emphasis on certain parts of their religion over others according to their own personal values. In fact it's impossible not to place emphasis on certain aspects of a religion or philosophy when adopting it - even religious zealotry implies an emphasis on perfect obedience and adherence. You can tolerate, accept, or even like a person holding an idea that you can't tolerate due to your own beliefs, for the personal values and virtues exhibited by the individual which are reflected in their emphasis of certain parts of their beliefs.