IMHO, some accusations of “both-sides-ism” are due to a confusion of people thinking that someone is saying that two sides are the same, versus saying that they think the same.
For instance, there is a big difference between saying “We are no different than ISIS” and saying “We think we’re the good guys and ISIS is the bad guys, but in their eyes they are the good guys and we are the bad guys.”
The former is equating two sides as being the same (and America and the West does not throw gays off rooftops or force women into slavery) whereas the latter is just a factual description of how people think.
For an another example - if someone says “Democrats and Republicans both regard each other as a dire threat to the nation that must be politically stopped at all costs,” that is not saying that both sides are the same, it is simply saying both sides think and feel the same. (Pew, Gallup, and many other polling groups have shown that both sides have increasingly identical but negative sentiments towards the other.)
Sure, there are some who genuinely do think both sides (whatever the issue may be) are the same. But there are others who aren’t - they are merely saying that both sides feel the same even if are not actually the same.