I don't know yet how well my flannel-backed quilts will hold up, but I do know that it shrinks like crazy in the wash. Prewash it twice, on a fairly hot wash, and put it in the dryer if possible. Also prewash any fabrics that you will be using in the top, as the shirt fabrics have already been thoroughly prewashed. I don't know if you were planning to make the top purely from the shirt fabrics, or to add in a few of your own for visual balance. It depends on the guy's shirt collection, really; some contain a great range of values and patterns, others don't.
Now I think about it, I could probably do a reasonably nice (if small) quilt from my partner's shirts, as he has plenty of black and white, and a good few in other colours and stripes, including that gorgeous green stripe which I adore - seriously lovely fabric! - and which he isn't that keen on. Although probably at least half his shirts are white and not that thick, which I wouldn't really want to be working with. But I really shouldn't be thinking this way!