Hank Morgan is trying to undermine the nobles in part because he thinks they are power hungry and that they are fooling the people into obeying them (with talk of things like divine right and such). He also thinks that they do not care enough about their inferiors. Morgan himself, though, has some of these same faults.
Morgan is clearly power hungry. After all, he is trying to essentially take for himself the power to remake all of England. He may be doing it for what he sees as good reasons, but it's still a sign that he is very ambitious. He is not above fooling people to gain power, either. He uses things like his scientific knowledge of the timing of the eclipse to make people think he is a sorceror. Finally, he uses his power in ways that are sometimes abusive. The best example of this is how he has Sir Dinadan hanged because he does not like one of the jokes in Dinadan's book.
In these ways, you can argue that Morgan is no different from the nobles that he is trying to undermine.