Hi Nichole.
If meeting
Rapunzel from Tangled is a must-do during your time at Magic Kingdom, I would suggest that you pick up a Times Guide as you enter the park, check the Character Greetings Times section and make your way to the Fairytale Garden approximately 15-20 minutes prior to the start of her first appearance of the day which is normally 9.15am.
You will find that the lines will get longer as the day progresses and more Guests arrive at the park.
As of 3 July 2011, Flynn Rider is no longer part of the Tangled play-and-greet at the Fairytale Garden in the Magic Kingdom. I can tell you that Flynn did appear alongside Rapunzel at
Mickey's Not-So-Scary Halloween Party last year and as you are travelling to Walt Disney World in September,there is a chance that you could attend one of these parties and he MAY be there.
The dates for that this special event will take place in 2012 have not been announced as of yet and purchase of an additional event admission ticket is required to attend Mickey's Not-So-Scary Halloween Party. If you are planning to attend, I would strongly recommend that you purchase your tickets in advance from the Walt Disney World website as some dates do sell out.
Wishing you a magical trip filled with memories which will last a lifetime!