I travelled for 2 weeks all through Xinjiang and talked a lot with University professors and other native Uighur during the Anniversary of the first unrestes, in July 2011.
The issue is that the Chinese Government is trying their best to "get rid" of the Uighur culture there. They want people to live in modern housing, intermingled with Han-chinese people. The old city of Kashgar for example is crubmling to dust because the Chinese government takes over all houses where the inhabitants die or move away, and turn them into a heap of rubble, not allowing anyone else to live there anymore. Like this they destroy the old city house-by-house. You can read more about this here. Here is a photo I took at the time. You can see the crumbling homes clearly.
This is only one example of a treatment that turns Uighur people specifically against the Government and Han-Chinese, not at all against foreigners. The reception that I received from locals during my trip was extremely positive and hospitable, specially from people you would simply see in the street (i.e. not people who would expect you to be a source of income in any way).
The risk you face is much more collateral. For example, you are not allowed to even have the tiniest of knives in your Check-in luggage when flying in and out of Xinjiang Airports. Further, the Government is worried that foreigners are actually reporters or do things that would hurt the image of the government. If you are around public places during the June/July months, you can see civilian chinese with batons in groups of 5-10 patrolling the streets. There is police everywhere. You feel much more threatened by those than the locals.