Petraeus' general worldview is you can't be successful unless local populations on the ground are to a degree on your side instead of passive or working with extremists. Part of that obviously involves respecting local customs and religious practices. For example, when that nutty "pastor" in Florida threatened to burn hundreds of Qurans a few years ago....Petraeus came out with
this statement. Sounds completely rational and routine, but never something you would hear from Flynn, Trump, Bannon or the rest of them.
Flynn is basically from the paleoconservative, Huntington/clash of civilizations school of idiocy that thinks calling extremism radical islam is some sort of necessary starting point to defeating it; whereas Petraeus has a Phd in International Relations from Princeton. Ideologically, they are light years apart.