Radicals always exist. Everywhere and in every culture.
Mainstream support of radicalism is what waxes and wanes. As iSm pointed out, these conflicts mostly started out as nationalistic (arguments over sovereignty and geography) and have turned religious as the secular government leadership has fallen aside. I would argue this is because the nationalistic argument and the fundamental religious argument have come into alignment, but remove that alignment and the radicals will once again be on the fringe. The mainstream may not entirely condone the methods but tolerate it because the goals are the same. As soon as the mainstream and the fringe have different goals, it'll break down.
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