Who are the real Jihadists?

The leader of the Iraqi resistance has identified the Iraq army as its enemy. As I recall, the original Jihad was when the followers of Mohammed were attacked by the infidels from Mecca and were enjoined to fight to protect their fledgling religion as well as their society in Medina. Why then does everybody assume that only the terrorists are the Jihadists?

If I were leading the Iraqi Army, I'd be invoking Jihad as the fight for the rights and freedom of the Iraqi people including their right to practice the religion they prefer as individuals. If God will judge each of us individually, does it make any sense to argue that any of us should be forced to live something that we don't believe? Cannot God see our hearts and minds?