OK, I'm going to be a bit contrary.
Your most likely minor problem is losing a seat cushion out of the interior. On mine, the rear center cushion gets a jet of wind at/under it from under the windshield and it has considered leaving the boat once or twice (but fortunately never has). One advantage of trailering with a cover is you don't have to worry about this. If you have a trailerable cover, take Sullivan's suggestion of Saran Wrap for the gunnels and put the cover on - it'll keep things a lot cleaner, drier, and help keep wandering hands from exploring the stuff in your boat.
I drag my boat all over the state of Arizona without any kind of gravel guard, and I've never noticed any kind of rock ding or even mark (lots of dead bugs, but that's a different matter). I simply wouldn't worry about this issue.
Your most likely major problem is going to be a flat or blowout. Make sure that the jack you take can get under the axle with a flat tire, and (as others have suggested) that you have a lug wrench that fits the trailer lugs. On my single-axle trailer, there is no known jack in the world that will get under the axle with the tire flat, and the jack I have won't lift the frame high enough to get the wheel off the ground. Consider bringing along enough foot-long lengths of 2x6 that you could create a ramp with them, place them in front of the trailer wheel, and then pull the trailer up on them to create enough space under the axle that your jack will fit.
Second major possible problem will be bearings. After the first 30 miles and then every time you stop for gas, put your hand on the hub. It'll be warm, perhaps uncomfortably so (120 degrees perhaps), but if you leave any skin behind or end up with blisters, somethings terribly wrong and you need to fix it before you go anywhere else. It's likely either brakes or bearings, but you don't want to pull it any further until you find out which and resolve their issues. Buying one of the inexpensive infrared thermometers like this
will keep your hands clean (and unblistered) when you do this check.
ALWAYS, ALWAYS use rear tie-downs, and make them tight. If you don't believe me, simply drive behind an untied boat on a rough road - the boat will be bouncing 2" off the bunks and slamming back down. You want the boat and the trailer to be a single unit moving together, not two independent units bashing each other. The boat isn't going to bounce off the trailer going down the road unless you're in an accident, the straps are there to prevent that pounding - and to keep the boat and trailer together in case of the aforementioned accident.
Don't drive too fast - higher speeds cause drastically higher tire temperatures and likelihood of failure. Make sure the tires are inflated to max sidewall pressure (cold), drive the speed limit or below, and your day will be a lot less stressful.