Causation theory is a complex science and involves philosophy and the social sciences. Causation is rarely, if ever, a black-or-white issue. The first to appreciate this was Robert Koch who discovered the cause of TB; in fact he had to formulate his postulates to convince his peer-group that he had found the cause of TB. Even then it took Robert Koch more than a decade to convince the scientific community of the significance of his findings.
The issue of causation theory has come up recently in relation to our posts on CCSVI. If you are interested in reading more about causation and causation theory, specifically in relation to MS, I would recommend the following articles as a starter:
Giovannoni G, et al. Infectious causes of multiple sclerosis. Lancet Neurol. 2006 Oct;5(10):887-94.
Giovannoni G, Ebers G. Multiple sclerosis: the environment and causation. Curr Opin Neurol. 2007 Jun;20(3):261-8.