Its not that they believe "differently" than we do thats the problem, its the fact that Muhammad made clear commands to make war with the unbeliever, to be unyielding with them and to let them find in you "hardness". The people who speak out against Islam are worried about the teachings of Islam, and solely blame Islam. Its not really a loving thing to speak out in defense of Islam.
If you were to do so for Muslims being unjustly attacked, that would be completely different. But any Muslim who commits murder in the name of allah, the teachings of Islam are entirely responsible for the attack.
And I was really sad to hear about this attack.