Somewhere I read, "If the Bible is the perfect word of God, then why don't any two people agree with what it means."
The "Rapture" is not just a single event. There are several interpretations of the sequence of events. (http://www.absoluteastronomy.com/topics/Post_Tribulation_Rapture) Supposedly, there is going to be a seven year period called "The Tribulatuion" when God will "remove his spirit" from the earth and wickedness will run rampant.
Some Christians believe that they will go to heaven before the tribulation, some believe during the tribulation and some believe after the tribulation. It's the people in the last group who arm arming themselves and preparing for war with the unbelievers.