I've not read any Autonomist literature, wouldn't know where to start to be honest, but what are the differences between Autonomism and Anarchism? Both appear to be anti-hierarchical, both seem to be anti-party, both seem to be against "respectable" bourgeois politics, both seem to be against vanguards, both seem to believe in the need for self-lead working class action, both seem to believe and put a lot of practical effort into pre-figurative politics.etc
So where do they disagree? Why would one identify as an autonomist and not an Anarchist?
I don't think you can really hold up 'anarchism' as a single ideology that 'autonomism' would disagree with. Autonomism is a specific historical development of Marxism (i.e. out of '60s Italian workerism) whereas 'anarchism' is a much wider category.
This might help for getting a better understanding of where autonomism came from: http://libcom.org/library/libertarian-marxist-tendency-map
Also Harry Cleaver's Introduction in 'reading capital politically' covers similar ground.