I would agree that it could be the shorts. However I think there might also be a couple of other things causing your problem.
The first thing that I will say is that a certain amount of soreness is almost guaranteed when you start putting in longer intervals on the bike. This is not to say that you are not having a genuine problem, but your ass will get tougher over time.
I have to disagree with dave in saying that changing saddle position should be an absolute last resort. I have had many experiences where changing the angle on my saddle even one click on the seatpost makes all the difference in the world. I have had seat posts where adjustments as small as 1 click would always have the saddle pointed too far up or too far down. Also, last year I set up my saddle position on the indoor trainer. This position worked just fine for me, until we got outside. Once we got on the road, the position was EXCRUCIATING! way too high. I had to stand for about half the ride. I will say that I doubt this is your problem, as I assume that you haven't changed the position since you last rode outside.
Saddle shape is also a huge issue. I assume that this is also not your problem if your saddle has always worked for you before. That being said, saddles do wear out over time. The foam padding gets compressed, and the plastic base will become flexible to the point where it doesn't provide proper support. This is a possibility if you have a really old saddle.
Before you invest money in any new gear, try a few things. The first is too give your ass some time to toughen up. Second, you can always borrow a pair of shorts from a teammate to see if they help (note: wash thoroughly before and after use for maximum STD prevention). Third, try a different saddle, making sure to keep the position EXACTLY the same as you have now (this could actually involve moving the seatpost, as different saddles could have shorter or taller rails, paying attention to fore/aft position is equally important). I highly recommend the bontrager inform saddles, and I could more than likely get you a loaner from the shop if you want to try one. Lastly, I don't recommend making any position changes until we get outside. What feels perfect on rollers or on a trainer will almost certainly be different from what feels perfect on the road. Which brings me to my final possible solution, see what happens on your first long ride outdoors. This discomfort you're experiencing could be a product of how your position changes when you are an an indoor trainer.