While nowhere near as common as Arab and Islamic terrorists, ultra-radical Jewish perpetrators of terrorism still exist. Meir Kahane and his followers are perhaps the best known of this sort, though Kahane has been in jail in Israel for several years now and his group is largely inactive. The paragraph in the NY Times article about how Israel has not confronted a Jewish terrorist group in 20 years show just how minimal Jewish terrorism is.
Regardless of whether one thinks the settlers are justified in living in the West Bank and Gaza, there is something to be said for their claim that the IDF does not give them adequate protection. Settlement infiltrations are attempted many times each day, with indiscriminately gruesome results if they are not prevented. Vigilantism is not widespread in the W. Bank and Gaza yet, but it could grow if militant groups succeed in more attacks against Israelis.