Well it depends hugely on what we're talking about. It can be a way to victim-blame the abused. No, don't ask (for example) why a woman tolerates her husband beating her, much less say she deserves it. But I sometimes feel like saying something similar to people who (for example) just don't bother to raise their kids properly and then complain that they've got a brat. If you tolerate your kids behaving unacceptably, you deserve the results you get. It's about power. Sometimes you have the power to decide what you'll tolerate, and sometimes you don't. This varies a lot depending on what the relationship is and various other circumstances (like, do you have the money to walk away etc),
In terms of wider societal stuff, I think it's quite a problematic term. It's creepy when people talk about "toleration" of different races, cultures, religions and suchlike. Because the word implies that there is in fact something bad or wrong about the thing / person being tolerated. Also that the other group really do (and ought to) be reliant on the goodwill of the dominant group that tolerates them. The existence / freedom / right of other human beings aren't for anyone else to decide whether they will allow.
We shouldn't tolerate abuse, sexism, racism, terrorism, paedophilia. From anyone. But as soon as we start applying the term to people rather than behaviours, it's a problem. And when we imply that anyone has the power to stop something unacceptable single-handed - to just declare what they won't tolerate and have it stop - when in fact they don't, it's a problem. Sexism often takes this form - saying she should have just stopped harassment or abuse single-handed, why didn't she stand up for herself, why would she put up with it etc. And there's a lot of overlap between this and the worst kind of selfish individualistic right-wingery that tells people that anything bad that happens to them is entirely their own fault and denies the existence of socio-economic disadvantage (and therefore of the need for everyone to work together to overcome it). Sometimes we need solidarity to stand up to the things that are intolerable. Sometimes we need laws. Sometimes we need to make radical changes to the way our whole society works. It depends.