"Islamophobia" is a myth invented to silence critics of jihad. If you dare point out the obvious connections between what ISIS is doing and the Qur'an verses ISIS is quoting, you will be called an "Islamophobe." A "phobia," however, is an irrational fear, and people's concerns about jihad are legitimate and reasonable.
Nevertheless, hatred of Muslims simply for being Muslims is a real phenomenon. I read comments regularly from people calling for violence against Muslims. Here's an all-too-common example. ***WARNING: GRAPHIC LANGUAGE***
Here's the key to remember. Islam is an ideology. It has no feelings, and has no special privileges over other ideologies. Islam has been put forward as the truth; hence, we are entirely justified in scrutinizing it with all the tools of logic, epistemology, and rhetoric.
Muslims, by contrast, are human beings, and human beings have rights. Among these rights is the right not to be killed for believing in a certain book or a certain prophet. While we may disagree with our Muslim friends about their ideology, disputes about ideologies should be settled through argument, not through threats or violence.