Its all in the shocks. TRD's come with bilsteins, non-TRD's dont. I think mine (04 TRD ex-cab) rides great on the highway even with 265/70/R16 Bridgestone Revos, all-terrain tire compared to the BFG Rugged Trails (all-season tire---good on the highway)
You better believe it. TRD Tacomas (previous generation -- 98 - 04) ride as rough as cobs on the highway. Not sure if the double cab would ride any better, but the extended cab will beat you to death on the road. Not only this, but they're downright dangerous when you hit a sizeable bump or pothole at speed while driving on the highway.
The TRD suspension is more than just shocks. It's an entirely different and modified suspension over the non-TRD. I think this was a $1,600 option in my '99 Tacoma TRD 4WD, and there is a reason for it.
But, take the TRD Tacoma off road and it's like flipping a switch. The truck becomes a different vehicle. Not only is this truck made to drive off road, but it's made to drive FAST off road. Also, the TRD rides like a Cadillac off road. This is what the truck is made for.
My advice is to look for a non-TRD Tacoma unless you really plan to take the truck off road A LOT! After all, that's what this truck is made for and if you never get it off road, you'll never be able to appreciate what it can do.
Incidentally, the new (05 and 06) Tacoma TRD Off-Road trucks ride much better on the highway than the previous generation.