Nunchucks, or any flexible weapon such as a chain can be tricky (and occasionally painful) to learn.
There are some simple steps you can take to get fluidity of motion in a shorter time.
1) Do your best not to "catch" your weapon, but instead, have the weapon land in your catching hand. Do your best not to have to adjust your catching hand. One of the easiest ways to practice this is a simple hand change in front of your body, vertically (don't whack your nose!).
2) Practice hand changes with your eyes closed. This will force you to "know" where things will be before they get there. It develops faster hand changes, and an intuitive sense.
3) Practice non-body checks - meaning the ability to halt the weapon's movement without the use of checking.
4) Practice mid-movement redirection. Meaning change a horizontal strike into a vertical strike, then back again and so on. The ability to change direction is essential.
5) Practice fluidity of motion. Create a sequence of movements which flows from one side of your body to the other which incorporates difficult but predictable movements.
For an example video which takes you through step by step, watch: MMA made EASY: Nunchuck Tutorial
(Make sure you have your annotations on, as they link to the next step in the series)