A couple of years ago a group of friends rode the Trace from Nashville to Natchez with support. I also live in Ridgeland, MS and ride sections of the Trace on a regular basis. I think the best months for a Trace trip are April into May and October. You are likely to catch some rain in April and May, but things are blooming along the whole Trace. October is much drier (unless a hurricane come through) and heat of the summer is off. I would avoid a trip in July, August and September unless you really like the heat and humidity. Riding in the middle of day in those months can be difficult.
While the TN section has few hills, there are no mountains or really big hills anywhere on Trace and large sections of it are really pretty flat. There are several bike specific campgrounds on the Trace. There are also B&Bs and easy access to motels in Tupelo, Jackson area, Florence and some other locations. You do have to watch out for commuter traffic around Tupelo and Jackson, which can be very heavy between 7 and 9 and 4 and 6. But the vast majority of the Trace gets very little automobile traffic. In the Jackson area between I-55 and I-20 generally gets alot of traffic, but from I-55 south for about 8 miles is closed until at least the fall of 2012 to repair a section of roadbed. That has really cut down the local commuter traffic. While that section is closed to vehicles, it is still open for bikes, which is really great for the local biking community.
To catch a plane from Natchez, you would need to get to either Jackson or Baton Rouge. You could probably catch a bus to either location.
Hope you have a blast. Its a fun and peaceful ride.