Actually there was/is no real reason as far as I know – ships below the waterline are painted with antifouling paint and I think in the past this had a high lead and copper (oxide) content and this made the paint red. These days you will find all sorts of colours below the waterline – but for commercial ships I would guess red is still the most common colour.
And this is what happens quite quickly if you don’t paint antifouling paint on the bottom of your vessel!!
