Hi Bethany,
Most families who have children on the spectrum report that Disney is a very user-friendly destination for their special kids. I'm one of them. I'm guessing you are concerned about how your son will do waiting for and riding the Disney buses, as for most of the resorts (which aren't on the monorail line), this is the primary means of transportation to the parks. We've never had any issues with the buses. They are very convenient and reliable, and run every 15-20 minutes throughout the day. I will say that during peak times, the buses can get crowded, and guests may need to stand. For the most part, guests are extremely polite, and offer seats to moms with small children. However, there is a possibility that you would need to stand with your son. If you suspect this might be a problem, I'd recommend travelling during off-peak times. Another option is renting a car and driving to the parks. If you are staying on-site at any Disney resort, parking will be free. Finally, you could consider taking taxis to the park (they are available at every resort and at the parks).
Another option is staying at the cabins at Fort Wilderness Resort. This moderate resort is located in the Magic Kingdom Resort area, and the park (which I'm guessing, based on your son's age, will be one of your favorites) is a boat ride away. The cabins are spacious, with a separate living room and bedroom and full kitchen. The extra space might help your son feel comfortable and give your entire family some addition room to spread out in.
I hope your little pirate and entire family have a magical trip!
Tanya