If you defeated "Moder", the fourth boss enemy, you can activate it's ability to get wind from behind, which is nice at times. It is the advanced solution to the problem.

However, if you are facing wind from ahead, there are basically only to ways to work around it: Lower sails and row the boat at the lowest speed setting, or zigzag sail ("to beat about" seems to be the term) - both may be achieving similar results, and it also is important to aim for using the long boat, everything else is even slower.

Personally I have encountered shorter stretches where wind was quite unfavourable, but I cannot say that it is doing that all the time, every time. Note however that sailing is only the second fastest traveling option, and is beaten using portals all the time unless you want to transport some basic metal ingots or ore.