My kids were right around the same age when we made our first drive from NJ to WDW (We've done the drive three times and have had no problems).
One thing that may help your 3-year old get through the periodic 'crankies' that can happen is to gather some things at the Dollar Store, or some inexpensive new books. Wrap them like presents and keep them in a gym bag in the car. When your child gets a bit restless, or at pre-set times during the trip, bring out one of the surprises.
"If you can be paitent and quiet until we get to exit number XX, you'll get a surprise!"
"When we cross into North Carolina, you'll get a surprise!"
Stuff like that to give your child something to look forward too in shorter increments of time, since the arrival at WDW is just too long for them to contemplate.
I'd also suggest going to your local library and checking out books on tape along with the print version. You can then have the tape 'read' the story.
Its really not a bad drive as long as you prepare for it, and realize that children that young will NEED to stop and stretch their legs. Plan for a break every four hours or so, have a ball to toss around or something else to let the older one be active a bit. Have a cooler with drink boxes or pre-made sippy cups set up along with snacks like cut-up grapes, bananas, goldfish crackers, etc. that you can easily get to. If the 3-year old is potty trained, pack the potty in the car along with Clorox wipes to keep it clean and maybe a sheet or large towel to create some privacy. This way, you're not tied exclusively to rest stops...when your child says "I gotta go!" you can just pull over, create your 'outhouse' and avoid accidents.
As I said, we've driven three times (and flown once)...and we'd do the drive again in a heartbeat. Our last drive was in 2005, my kids were 14 and 11 at the time and they really enjoyed it. "Forced Family Time" can create some very special memories.