Alan- I've done quite a bit of studying on this for my own line of ship models and flags, and have found that other than the Venetians, there was no predominant or consistent color scheme to the ships themselves. The color red ochre (barn red) was used more than any other color according to paintings of the period and models of galleys that I've seen in Venice. Red ochre was cheap and not fugitive in nature,(didn't fade) so was a good choice. Plus I am sure it made the ships go faster!
Other earthy tones like yellow ochre and burnt umber it seems were also used- as well as what ever color the dark wood is (I'm assuming natural wet wood?)
Here's a good reference image
link
That being Said, and as Prince Albert's Revenge mentioned, other colors of green and blue also showed up. There was even one notable Corsair who painted his entire ship and sails all black.
I tend to "hollywood" up my ships a bit with a predominance of green and blue for my Turkish fleet, and red, yelow ochre and natural woods for my holy league fleet. This picture of a Lepanto battle illustrates the look pretty well.
While doing research for flags and awnings, what really struck me the most was how much red was used by the Turks for their banners, flags and pennants. I thought it would be mostly greens. On the flip side, one of my customers sent me an image from a period wood block print of a Knights of Malta Lanterna galley (painted red) with green masts! Artist's license or historical representation- I'm not sure, but I'm definitely painting one of my ships that way!
Hope this helps- looking forward to seeing your fleets in action
Cheers
Thomas
skullncrown.com