I know I might get hate for this but I feel it needs saying. For it to be fully understood there has to be a distinction made between different parts of the debate on Islam. Most notably 'Muslim' 'ISIS and other terror groups' and 'Islam'. Muslims are followers of Islam, ISIS are a Islamic fundamentalist terrorist group and Islam are the teachings Muslims follow.
Firstly it is important to vehemently oppose Islamic state whose views and actions are truly deplorable. It is just as important distinguish that most Muslims oppose ISIS in the same way that most Christians oppose the KKK and they should not persecuted as that only leads to further radicalisation.
However, I believe we should also attack some of the stricter teachings of Islam , like the persecution of homosexuals and oppression of females which have lead to appalling human rights abuses in countries like Saudi Arabia. For they are contemptible in the same way fundamentalist christian views. The only reason these views aren't challenged is I think not political correctness but rather the left sees it as contradiction with their argument of tolerance towards Muslims so avoids it. Yet the only reason for this is that Islam and individual Muslims are too often conflated by the right.
To confront the issues of Islam we have to look to the past and Christianity. Many Christians today need to contextualise the world and realise that only a couple of hundred years ago Christianity and western society had a similar backwards philosophy to Islam on many topics such as homosexuality, women's rights and capital punishment which many Christians now rightly oppose. So how did Christianity change and with it western culture?
The origin of modern western society comes from the enlightenment and the realisation that every man is equal, which lead to democracy. Then slowly society became more accepting: women's emancipation, gay rights, and racial tolerance followed (although these issues are still not fully finished). This shows the only way to sort the problems of Islam is through better education and increased exposure to western values and through time less and less Islamic fundamentalists will exist because most people whether Muslim or not are good people and this leads to progression to a more tolerant and loving society as they realise the problems with their views.
tl;dr: Fundamentally, Muslims are good people so naturally Islam will progress to be more tolerant like Christianity did.