My description of what I think Merlin's thoughts on Uther are, and Uther's irrational hatred of magic.
R&R? I know you love me. :)
Being Arthur's lackey was nothing to get particularly excited about; Arthur was The Once and Future King of Camelot, and Merlin was a peasant from a different kingdom. It's not that he was ashamed of being a servant, because he honestly wasn't. It was saving Arthur's life time and time again, getting no credit whatsoever because he couldn't take it, because Uther Pendragon hated magic and the people and creatures that came from it and practiced it more than anything else. It was being required to hide who he truly was out of the fear of dying. The second any royal in Uther's court had an inkling that Merlin practiced magic, his head would be off. They were very few people Merlin had the pleasure of encountering that shared his ability, and fewer still of those who could understand the burden he carried. Yet, even he understood there were many who had it worse. There were the sorcerers who were hunted in every corner of the five kingdoms, forced away from all they loved and into hiding - here he thought of Balinor, of course; his reunion with his father was far too short lived. There were those who fell prey to bounty hunters, caged and sold to Uther like they were nothing more than a prized chicken, and those cursed to terrible fates for innocent and unintentional mistakes.
Years before Merlin came to Camelot, when Merlin was merely an infant, Uther brought about the Great Purge; he executed everyone who practiced magic or anyone simply suspected of doing so. He believed that magic was what made people evil; he believed it warped and manipulated a person so much that goodness no longer touched them, but Merlin knew the truth; the ability didn't make a person evil. Everyone has goodness and evil inside of them, and those who choose to act on the evil and push the goodness aside were the ones that practiced dark magic. The magic is only as good as the person who holds it.
While Merlin himself didn't originally know what fueled Uther's hatred, Analise, whose specialty in magic was memory charms and unlocking the secrets of another's mind, eventually clued him in.
When Uther wanted an heir that his wife couldn't give him, Nimueh, Uther's friend at the time, used magic to give him just that. Uther's wife Ygraine died giving birth to Arthur; that was the balance of the universe. In order to create a life, in this instance, Arthur's, there had to be a death in its place, that of Ygraine. Convinced Nimueh had done this intentionally, or something of the like, Uther became furious, seeking retribution for his wife's death, which was the very start of the Great Purge.
It all gave Merlin ample reason to hate Uther, and rightfully so.
But he didn't. No, truly, deep down, he knew he didn't hate Uther.
Merlin couldn't believe that the single occasion of a misuse in magic justified the killing of hundreds of sorcerers and brilliant creatures of magic and an outright hatred of the entire practice, but he soon learned for himself that when someone takes away the woman a man loves, there's nothing he wouldn't do to get her back.