I do both depending on whether we take the motorcycles or not. If we are just going for a weekend or extended weekend and are not going to take the Harley or the son's Buell then we just flat tow the Jeep.
Personally I prefer to tow the trailer as it is nice to have a rolling shop with me and to arrive with everything clean as you back it out of the trailer. We used to just use the trailer for towing our sand toys to the dunes for a weekend of playing but a few years ago started towing it more and really like towing the trailer.
Like others have already mentioned fueling must be done in the semi/truck lanes at the truck stop as manuevering around with the autos is a pain. Some campgrounds do not have long enough sites and you must unhook in a designated drop area but I have found that the exception rather than the norm. Some campgrounds will not let you have your trailer at your site even though the sites are plenty long, Las Vegas Outdoor Resort for example. When we go there we have to drop into a trailer parking area before going to the site even though the sites are more than long enough, it is just their policy, no trailers allowed at the camp sites.
We just returned from a week long trip to Ouray, Colorado and we towed the trailer with the toys inside. The trailer was loaded to just over 12k pounds and it towed great. Slowed me a little on the grades but not much more than flat-towing the Jeep. It was nice to have the motorcycles there and the Jeep, although the first three days we had rain so we did off-roading in the Jeep I was beginning to wonder if we would even get a chance to ride the bikes. Finally on the fourth day the weather was absolutely fantastic and we rode the motorcycles over to Silverton for lunch and then the next day to Telluride and wandered around. The wife thought it was kind of nice to be able to have both the bikes and the Jeep on the trip.
Our trailer is a 26' Haulmark Edge. When we ordered it I had extra height added along with an extended tongue, two 500 watt halogen lights on the curbside, L-shaped workbench, flourescent lights, ATP flooring and two 7k pound axles with 14 ply tires. The trailer measures an overall length of 31' and when hooked to the coach we are 72' bumper to bumper. The rig handles fantastic and is actually a joy to drive, you just have to think your way through fuel stops, lunch stops, parking lots and campgrounds a little more than when not towing but overall not that big of a deal.
I would not and do not tow the trailer if we are only going to be changing campgrounds every day to two as that is a PITA loading and unloading everything. Just the Jeep is not that bad but with the bikes it takes a little longer to make certain everything is secure. Flat-towing is much more convenient for quick trips or multiple stops on a trip. Just my opinion.
Mike.