The best way to prevent nails from sticking out of the eaves is to use shorter nails. But you need to be careful as shorter nails can endanger the structure of your roof. If the fixation is poorly, then you should try another method.
Bending the nails
Simply bend the nails down with a hammer, but be careful not to damage the eaves. You can then paint the place.
Adding a board
Another nice option that you can consider is adding a board that will cover the nails. It requires some measuring, cutting and standing on tall ladders. This will repair the bad look resulted from the nails.