The primary concern with Autism Speaks in my opinion boils down to 3 primary reasons:
1. They have no actual autistic people on in their leadership, they really represent the families of (usually servery) autistic people and not autistic people themselves. This of course means their name is a bit of an oxymoron.
2. Only a tiny portion of their funds go to actually helping autistic people (less then 1% I think). The vast majority of their funding goes to funding research with the aim of developing a genetic test that will prevent autistic people from ever being born through selective abortions. This is a major concern, since it effectively tells every autistic person that they shouldn't have been born. You'll want to look up their financial report for 2007 for hard evidence here.
_________________
The improbable goal: Fear nothing, hate nothing, and let nothing anger you.