Well, define "uncomfortable." The cleansing solution is a buffered normal saline (neutral pH with the same water content as human body fluids). If you mix it too strong or too weak, or if it's too hot, it will sting a little (like pool water). If it's properly mixed, to me it actually feels good on the sinus tissues.

Sure, you have to get used to the idea of water up your nose, and there is a feeling of fullness while you're irrigating. But millions of contact lens wearers had to get used to the idea of sticking our fingers in our eyes twice a day. And that stings a LOT if you have the wrong something on your fingers. Not a lot different IMO.