I made a John Deere Quilt, using BOTH cotton and flannel fabrics. It was a tad tricky. As long as you pre-wash it the shrinking wont be an issue. However, the flannel still stretches alot easier than the cotton so beware of that when you go to cut/sew/iron the seams. It's tricky, but not impossible. Here's a picture of mine that I made for my little boy: Click image for larger version. 

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(Hopefully that picture attached correctly) But the flannel fabrics in that are the light blue tractor pattern, and the green and blue plaid pattern. The rest are cotton. So as you can see I didn't use much, but it just goes to show you its not impossible. I mainly wanted to use some flannel for the mere fact that I made it as a baby quilt for my son so I wanted the textures to be different for him.

Good Luck!