I think a lot of folks can't tell the difference between the majority peaceful law abiding Muslims and the terrorists because they don't want to. Its just an easy way to justify paranoia, ignorance, and flat out hatred.
The major difficulty with this statement is that, for the past two years, we have seen so little evidence of "the majority of peaceful law abiding Muslims" that their existence has been logically called into question. What we have seen is the government and the media giving deference to organizations, such as CAIR, ISNA, AMC, that have been proven to have terrorist/extremist ties, and who are attempting to silence criticism of their highly questionable activities with cries of "racism" and "persecution."
What you are seeing is backlash effect, as the evidence of the senses -- in the form of violence, rhetoric, betrayal, and printed materials filled with naked hatred -- overwhelms political correctness.
To use the words of Robert Spencer:
The issues here are too important to be relegated to politically correct silence, wishful thinking, or lies of intimidation or politeness. It is incumbent on us to look squarely at the truth."
That "us" includes Muslims in America.