It is upsetting to submit in prayer "Thy will be done." We don't often pray for God's will but for our own.
At the same time, it can be comforting to know that His will indeed will be done, and-- whether we know it or not--it is for the best.
If God is omniscient, he knows more than I do or ever can. I must admit this when I'm at a crossroads of faith. I must rest assured that no matter the hardship for me or another whom I love, it is part of something bigger than I can fathom.
I don't have to like God's will in a temporal way. In prayer I might even submit a list of grievances. I think God understands and forgives such insolence. Nevertheless, despite my misgivings I should end every prayer with "Thy will be done."
In the end, His will is superior to mine, whether I like it or not.