Jihad is an important concept in Islam, war is not.
The word jihad is often used in the context of internal and personal struggle, and physical (or external) jihad becomes the struggle against oppression or prosecution.
Perhaps what changed between the past and today is the shift in focus from an 'inner' jihad to an 'outer' one. Militants justify their violence with the chaotic events of the last century; these are perceived as oppression, much of it due to western countries.
For more on the concept of Jihad: http://en.wikipedia.org/wiki/Jihad