I fully agree, but put yourself in their shoes for a minute...
You want to feel like you belong and that people don't look upon you with scorn, hatred, fear, or apprehension. And yet "followers" of your religion keep doing stupid shit internationally that does nothing for your image, to the point that even when you cry out against the attacks, no one believes you because(as you've already said) the outcry came too late, or people just don't believe you because your religious fanatics are always the ones to blame.
It leaves Muslims feeling ostracized, despite their best efforts. I even talked to an Imam about this in Ottawa, about why the outcry always comes late, or why there seems to be a lack of Muslim outcry, and he got really squirmish and this is what he said: "Well, I don't want to really put the blame on any one particular group, but a lot of us feel it is because of the media. They don't report on us a lot unless it involves the followers of a more fanatical branch of Islam." He was really uncomfortable placing blame on the media, even though that is clearly what he felt.
So because of all this, Muslims end up feeling like they are the only friends and family they've got, which leads to isolation and a lack of understanding and acceptance between Muslims and the ROC. Due to this isolation, it leaves a lot of Muslims starting to wonder if maybe just maybe the extremists have SOMETHING right.
From my experience in India, Muslims and Hindus on the personal and societal level tend to get along. My Aunt lives in Nizamuddin, which is a heavily Muslim part of New Delhi, the Capital of India. People leave Muslim and Hindu temples and shrines alone, and even allow visitation. For all the talk of not allowing infidels to enter holy sites, my cousing Hugh and I along with my Aunt and her daughter had no problem getting into very holy shrines of religious and spiritual leaders. My aunt wore a headscarf, but she's always done that since she's eccentric, and wears Indian clothing, so a headscarf is common for her.

We walked around, and were treated excellently. I got ripped off once on a deal, but I didn't want to cause a ruckus, and it was the equivalent of two bucks anyway, so whatever.

Other than that, my experience and association with Muslims was perfect. I even talked to them about the relationship with Hindus and Pakistan/India conflict up in Kashmir.
The fact of the matter is that the people don't care that much, but the politicians do. Muslims who are in India just want to live in peace and be left alone. Unfortunately however, conflict breaks out. Hindus and Muslims have been either killed or severely beaten simply because of their religion. The greatest known example of this was during India's partition, and there was massive rioting where dozens of Muslims and Hindus had been killed in Southern India. It took Ghandi starving himself to get these people to stop the senseless bloodshed.
It's a very complicated issue over there. The whole "Muslim debate" is certainly one of the more complicated ones the world has seen so far...