The parallels are better between islam and protestant churches because both of them are decentralized.
Do we have radical fringe groups who believe that homosexuals, muslims, and jews deserve death, though they stop short of acting on it as that would be the end of their organization? Westboro baptist church comes to mind and they are protected by the US constitution for as long as it remains just talk.
Haven't we had in the relatively recent history radical christian churches killing doctors who perform abortion?

Of course, we have to go before we outlawed murder based on religious belief and decided that we'll be secular countries.
But at the time the US constitution was written US didn't make it its business to tell other countries they need to act the same.
We may want to turn a blind eye between the similarities between christian and muslim beliefs based on the temporal separation, but what does that accomplish other than making us think we're superior. In contrast if we see the parallels we have at least one path that has been proven successful.
As I said, one way or another we'll get there or kill each other in the process. We became peaceful and tolerant society despite all of the extremists and all the bloodshed in our history.

The current radical islamic theology is not an invention of ISIS or AlQaeda. It's an invention from the circles of the dominant sunni sects in Saudi Arabia. The Saudi government stays in power because of the agreement with those clerics to turn a blind eye on their extremist views and practices. And we, especially the US provide military support for that government protecting it from the external threats.

Nothing will change until the roots change but that's a lot harder and complicated than 'kill them all'.

Yes, just like slavery is complex issue so is islamic terrorism. We solved our issues with slavery, it took us a long time and a lot of blood and treasure; muslims need to solve their issue with their radicals. Solving it for them means colonizing them and developing their societies to our standards - is that even possible?