I see a lot of questions about this issue from time to time.. I do know that one of the common mistakes is to run the trailer too deep into the water while loading. If the front under the bow can hit the bunks before you get close to the windch it will naturally push the bow of the boat high enough to avoid the problem in many cases. The steepness of ramps affect this some too. There are places and times at various water levels where I've had to start up on to a shallow trailer snug it up with the winch, then get out and back the trailer down under a little more and repeat this untill loaded. Of course, this pocess is more simple with a partner driving for you. I think there is a common tendancy to put too much of the trailer in the water to load. Take the time to experiment with this and I think you will see what you need to do to avoid the issue.
Following up on what Larry said. Most bass boats have 4 bunks on the trailer. 2 longer ones in the middle and 2 shorter ones on either side. My general guide when loading a boat I am not familiar with is back in so the front tip of the shorter bunks is just barely sticking out of the water. Then I approach the trailer at an idle and pull it out of gear just before it contacts the bunks. The boat will settle itself in the bunks. Then I make sure the motor is straight and use it to push the boat up onto the trailer until the bow loop contacts the roller. After doing this a few times, you find the sweet spot. If you have a strong cross wind or current, then put the trailer in a little shallower, then hit the bunks under power and get it settled straight, then have the trailer backed in a little further and finish pushing it up to the roller.