I love cheese on my omelets as well and I don't seem to have any kind of intolerance at all. Milk and cheese tend to make it harder to loose weight though. So, if you're trying to lose weight still, then you might want to cut out the cheese. If you good with your current weight or you are still losing while eating it then keep it up. Personally, I've cut out milk entirely and reduced my cheese intake down to a minimal level.