From a rhetorical standpoint, responding to this shooting with "not all muslims are bad/I hope they will be okay" is a serious mistake.
This is fresh news. Many people died. They need to be mourned. The salient abstract issues are the right to free speech and how these secular rights interact with extreme religious beliefs. This should be plainly clear to anyone observing this.
Turning it into "don't persecute Muslims" not only draws more attention to whatever religious nonsense these whackos happened to believe but also makes the speaker appear callous and self-centered. If the speaker is muslim, it places their religion above the other more important issues (which is arguably the kind of thinking that lets jerks think they're above the law).
Responding to any tragedy with "it's not my fault" is a terrible strategy.
You're missing an important point here, which is that it doesn't take into the account the positions muslims have in Western Europe these days (and I honestly don't know how it compares to the US situation). Muslim immigration in recent years has been high, and they're a significant part of the population of many of the countries over here (here being the Netherlands, but also countries like Germany, Belgium and France). Tensions have been high, especially after events like these. We had our own national tragedy when Theo van Gogh, a Dutch satirist was murdered for pretty much the same reason these people have been killed - and after that violent incidents and intimidation against Muslims who had nothing to do with any of it significantly increased. I'm talking people damaging mosque's, public harassment on the streets, bricks thrown through windows. It may just be a minority reacting like idiots to incidents like that, but it wasn't a good time to be a muslim in my country. My girlfriend happens to be Muslim, and while she didn't experience any harassment herself (she doesn't 'look' Muslim - meaning that she doesn't wear a headscarf), many of her friends and family members weren't so lucky. These are just normal people, who are just as disgusted and shocked by news like this as you and me, but reactionary idiots see every Muslim as a supporter of behavior like this, and that can lead to very dangerous tendencies. And tensions towards Muslims always increase around events like this - always.
Of course the actual victims of this crime shouldn't be ignored or forgotten, but Muslim leaders condemning these crimes and Muslims and non-Muslims speaking up about this is absolutely essential. History tells us that the risk of this leading to violence and intimidation towards regular Muslims is pretty damn high, and that's something that's worth trying to avoid.