Alcohol is good at killing nasties.The Westons cider factory is just down the road from me, they had an open day a while back, showed the start of the process with a guy picking up a load of fallen apples with the front bucket of a JCB - complete with all the dead leaves, sheep crap etc. All adds to the flavour I suppose...
I had a good chat with a brewer a few years ago who had previously run a mobile bottling plant before setting up his own brewing company.
Somebody had asked why he only done low alcohol beer, ad it was because alcohol free beer is quite risky to produce. Everything in the production line has to be sterilised, whereas with normal alcoholic beer, you can be a lot more lax with hygiene as the alcohol itself disinfected things.
He also said, you'd probably be shocked if you knew the lack of hygiene some small brewers had. He'd refused to bottle beer at some places due to conditions, and the owners would just get somebody else to bottle it.