At first it bothered me, to be honest. But, after a couple of years, and seeing my digital collection grow, I became at peace with it. I am slowly buying back issues of Uncanny X-Men on Comixology. My goal is to eventually have the entire Uncanny X-Men series digitally.
But also, with the reboots and Marvel NOW's happening, there have been plenty of opportunities to "start fresh" digitally. So I don't miss the paper comics at all now.