The following graphic from the NY Times demonstrates a couple things pretty well.
First, we see a major bump in the number of bias complaints by Muslims after September 11th. While unjustifiable, these are at least socially understandable. Second, we see a more modest rise that coincides with the recent economic decline. Discrimination against those seen as "others" increases when natives feel economically threatened. Those fears are irrationally directed at the most easily identified other, not to the actual causes of dis-ease. Finally, we can see an overall upward trend net of these two factors. This is probably due to rising levels of awareness of and interaction with Muslims and Islam.