The italian case does not offer causative proof that the MMR vaccine was associated with autism. Indeed, the overwhelming weight of evidence, of robust clinical trials, shows no such link.
More generally - I think science can be poorly communicated by the media, who prefer to look for some kind of sensationalist angle in any story, or seek to divide the world into those things that cause cancer and those things that do not. Scientists themselves and academic institutions do not escape blame either - too often they spin a mediocre paper in order to create interest or generate more funds.
I also think though that our science education is pretty poor, although i can only speak for the UK.Many individuals seem, to me at least, quite shockingly ignorant about basic scientific and medical principles and facts.
And then - We have the increasingly jaded and suspicious view of government, as either being incompetent or complicit in conspiracy, so government is now mistrusted on, well, virtually anything you care to mention :)
Vaccines are a particular issue though I think. Parents generally wish to protect and shield their children from harm and pain and hurt, and can feel guilty about taking their children for a procedure which causes pain, albeit usually fleeting - so when governments are mistrusted, and doctors and some pressure groups claim that vaccines can do long-term harm - well it becomes easier to do nothing.