plain and simple it is both bacterial and autoimmune as for as the course of the disease. this does not mean it began due to bacterial infection. the bacterial element is a dysregulation of the bacteria in the gut. the gut bacteria can affect the immune system, and the immune system maintains the balance of gut bacterial.
something like c-diff UC is due to infection. In that case there is a specific infectious agent that needs to be eliminated. The stuff in probiotics are necessary bacteria (consider colonization rather than infection).
You can get a lot of education on this topic from the special issue of Science on the Gut Microbiota
www.sciencemag.org/content/336/6086.toc#SpecialIssue