Part of it is media. The power of media and speakers to influence thoughts, emotions, beliefs shouldn't be underestimated. Propaganda is really strong and the media has been pretty effective in saying while we all stand together, Islam/Muslims = ISIS. They don't focus on the vast majority of Muslims because they're not causing problems or making a splash on headlines.
I thought the Guardian's did a decent job in jihadists' manifesto. Their tactics are really shrewd. They're not that dumb but play to our weaknesses. I remember Al Qaeda saying they want the US involved in Middle East, take away their freedoms, bait them to destroy current dictators to create a vacuum of power that jihadists can then go in and occupy.
President Obama (although I've criticized him before) is smart in not falling for the trap and is refusing to send boots on the ground. Very smart, wise move.
The problem w/jihadists and people understanding/accepting moderate Muslims is that the terrorists in many attacks were moderate Muslims. Anyone watch the interview of the brother? Very normal people. In fact, many acts of carnage (shootings, terrorists) were committed by people who were thought of as normal by the people around them and express shock. "OMG, how did this happen?" Not so hard to kill lots of people. Automatic weapons, ease of information, bombs, vicious cocktail. Who knows, maybe nukes could be next.
Merkel letting in more of these refugees increases the potential candidates for terrorism. Sure they're moderate. But they can transform to be dangerous. Sure cells are okay, but can transform into cancer cells.
While Muslims aren't the only ones capable of carnage (Oslo Norway, 2011), they are responsible for many attacks. I think some people need to watch VICE's coverage on Islam in UK. It's nuts.
And remember, many "moderate" Muslims joined ISIS in Syria. Many normal people became jihadists.
Also intriguing is that many of these people are poor, no direction. European economy isn't great and poverty, isolation, frustration, are ripe ingredients for extremism to take root.
This won't be the last attack either. I expect this to be an occasional occurrence, even after ISIS is defeated. Since extremism isn't just ISIS or Al Qaeda.