There is no doubt this is based on separatist activity.  I have found the claims of the Uighur Protesters contradicted in so many ways.

A few interesting facts:

1. Xinjiang has 13 Ethnic Minorities, most of which are Muslims, yet only Uighur's are protesting and they are the majority in Xinjiang

http://www.china.org.cn/english/MATERIAL/139389.htm

2. Uighur's are exempt from China's one child policy

3. The two Uighur's killed in the Shaoguan Toy Factory fight were not accused of rape.  A Han was spreading false rumors on the internet and arrested for it.  This arrest came before the protests.  If the government does not like Uighur's they would not have arrested this person.

http://news.xinhuanet.com/english/2009-06/29/content_11616274.htm

4. Relatives of the 2 dead Uighur's condemned the riots and say there is no connection to the Urumqi riots.  The body of one Uighur was flown back the same day for burial and allowed to be buried according to local customs.

   "I believe the government will handle the brawl appropriately," Turdi said. "Why did the rioters destroy our beautiful and peaceful Xinjiang region in such cruel manners?"

http://news.xinhuanet.com/english/2009-07/06/content_11663627.htm

5. Uighur's in the mainland have restaurants and mosques.

6. If Uighur's are being abused why were the protests only in Xinjiang and not in the mainland ?  Clearly the protests were organized, but for some reason whoever organized them wants the focus to only stay on Xinjiang.

7. Some Uighur's view Xinjiang as their own country and dislike any foreigners living there.

http://www.cfr.org/publication/16870/uighurs_and_chinas_xinjiang_region.html

8. And for those who don't know, Rebiya Kadeer was one of the richest Chinese citizens during her time, and she was honored by the government and sent to the "National Assembly" and also made a UN delegate.

All of these facts really fly in the face of Uighur accusation and simply defy logic.  I am a Han Muslim who has visited Mosques throughout China and my impression and experience tells me that Islam is more respected in China than anywhere else in the world.