This is on the right lines. If you read a book called "The Looming tower: Al Qaeda's Road to 9/11" it tells the history of the development of Islamic fundamentalism & paints a picture of radical Muslim political thinkers who objected to their countries (mainly Egypt at the time) going down the route of Westernisation. They espoused that Muslim majority countries should be run on a religious basis, not as what we consider to be social democracies. Throw the doctrine of Salafism (which is a Sunni ideology) into the mix and their aim is to see countries run on a much more conservative (i.e. strictly interpreted) basis than it would be under Shia or other forms of Islam.
So Iran, which you mention, is sort of a theocracy but it's Shia-dominated rather than Sunni. So the concept of Jihad as it exists among some Salafists isn't a factor in their belief system. They do however project political power to support other Shia's against Sunni oppression. Even among Salafi adherents, the majority don't get involved in politics, some do but don't resort to violence but a minority become jihadists. So you can't even blame Salafi's as a homogeneous group.
Compare that to Christianity, where the majority follow their faith peacefully, some (particularly in the USA) use it to justify their political beliefs and some, like the Westboro Baptist Church, are religious extremists. They're not violent ones but there are people who attack abortion clinics and have even murdered people who work at these clinics in the name of religion. Can we blame Christianity & Christians as a whole for those people? Should all Jews take the blame for the actions of Israel in Gaza or those individuals who kill Arabs? No we can't although that we have to recognise that religion gives them a platform or excuse for the way they formulate their twisted beliefs.
Let's also remember that Islam is only about 1400-1500 years old. Think back to Christianity in the Middle Ages when there were schisms, persecutions of Catholics & Jews, burning of witches and not forgetting the Crusades just a few hundred years earlier. Islam has evolved in an environment unused to democracy and where many of its adherents live in a world that doesn't accept or understand many of its beliefs. Judaism has followed the same path and while many of the most religious literally believe in the Torah and all its associated works, it's sort of come to terms with the modern world. Many of the most religious have as little contact as possible with the outside world, they don't have TV's, radios, the internet or newspapers. Their kids aren't taught in English, mainly study religious texts, do little maths and certainly nothing scientific that might conflict with the word of God, don't learn about other religions or sex education. Religiously they're just as extreme as the Salafis but they don't have a political ideology that drives them to jihad. They believe in the coming of the Messiah and that religious devotion, rather than violence, will hasten that.