I've towed with an open trailer for over 20 years. This past year I bought an enclosed, but still took a trip with my brother on an open trailer. So you can say I have become an expert on covers and taking care of my sleds, as you will find very minimal rust or corrosion on my sleds, and they still look like new throughout. Out of the 4 sleds I own, and the sleds I have owned in previous years, I have used several different covers. One of the best covers I have owned was a Scheer Madness Body Cover. Unfortunately this company is out of business(probably due to enclosed trailers), but you can occasionally find a used one on Ebay. The Extreme and Body covers from the sled manufacturers are also great covers, but some do not offer the full protection I would prefer. Here is a break down of the sleds I have and the covers I use.
2007 Renegade 800 & 2014 Renegade 900 Ace: I use the Skinz cover, as this was the best cover on the market that covers the sled completely from front to back. It is a spandex type material, and needs to be stretched while putting on the sled. It does a great job and looks great. To get the perfect fit, and avoid the ballooning effect, I have to tighten the cover as tight as possible, which is ok, as it's made out of Spandex, and can handle the stretch. I also add a strap in the middle, looping it through the front of the rear suspension, and over the front part of the seat, just behind the handle bars. This keeps the cover from blowing up or ballooning excessively when towing on the high way. The older cover needed a small repair, but Skinz gives you a repair kit with glue that works great. At this point in time, I believe the Skinz is the best cover offered, but it will take time to get used to it. It will tighten back up after washing, so getting used to stretching it out, and knowing it will not rip might take time. I do use under covers on the hood and windshield.
2003 XC500 - just picked up a used Scheer Madness cover off of Ebay. Fits this sled perfectly, front to back, covering skis and all. It is a very thick cover, and if kept tight, will last forever. These covers were made specifically for different types/styles of sleds. This cover only works on Polaris Edge type sleds, or the older MXZ's, not Rev's. They used to make one for the Rev's, that covered everything but the back part of the tunnel and bumper. If this company was still around, they would be my first choice in covers.
2006 Freestyle - Purchased a Ski-doo cover for the Tundra. Fits the sled well, but not a body cover. The cover has held up great, but I would prefer a body cover type, rather than leaving the skis and suspension somewhat open for salt or road grime. Quality cover, but does have some excess slack that will flap in the wind. I run a strap from under the sled and over the top between the windshield and handle bars.
Overall, many covers will work. The biggest issue to making them last is to avoid the excessive flapping in the wind while trailering. Adding extra straps to prevent this, and help keep the cover tight is key. You can buy the cheapest cover out there, and it will last if you keep it from flapping in the wind. I bought a universal cover from Parts Unlimited for my nephews 1980 Enticer, and it still looks like new after several years towing on an open trailer, because I took the time to strap it down tight, and use extra bungee cords or straps. Your best bet is to buy a cap or an enclosed trailer, as covers take a lot of time to get just right for 7 hour hauls up to the UP of Michigan. But if you do it right, they will last forever. But when towing 4-5 sleds, I found myself spending an excessive amount of time covering the sleds. Then when I returned home, I had to wash up the sleds asap, to get the salt off them, and avoid the corrosion from setting in. Then after I washed them, I would soak them down with WD-40 to protect them. It just took up too much time, and that is why I decided to buy an enclosed trailer. Using an open cover for 1 or 2 sleds is fine, not that much work. But when you go to 3 or more, then your spending too much time loading and covering the sleds just right, and way too much time cleaning the sleds, cover, and trailer when you return. So much easier with an enclosed trailer, no salt touches the sleds, so you can wash up the trailer, and get to the sleds when the time is right, as well as the weather.
Hope this helps.