Why not have your protagonist be wrong and misguided in his opposition to your fictional world government? Possibly the protagonist has strong and convincing personal reasons for wanting to overthrow the world government, but by the end of the novel or series he might realize he was wrong, or the readers might realize he was wrong.
For countless thousands of generations humans and their primate ancestors lived in small bands of hunter-gatherers and conflicts between two groups often resulted in the extermination of the loosing group as they might have lost their hunting grounds and all starved to death, or been captured by the winners and killed and eaten.
Thus the groups which survived by wining were likely to be those that were most patriotic for their bands and which tried harder to win than their opponents. For hundreds of thousands of years humans have evolved to be more patriotic toward their small groups and to feel that they will die if their small groups are defeated in conflicts.
And when larger societies formed, humans became patriotic toward those larger societies, and continued to believe that they had to support those societies in conflicts with other humans, even though the results of losing wars between nations are usually much less dire than the results of losing wars between hunting bands.
Humans have the built in flaw of being patriotic, loyal to a small subset of all humans, and being willing to fight and kill for that small subset of humans in conflicts with any or all other humans.
The function of independent and sovereign national governments is occasionally fight wars resulting in the deaths their own citizens and the citizens of other independent and sovereign national governments. Sovereign and independent national governments are killing machines.
In recent decades and centuries sovereign and independent national governments have started to do a lot of good things for their citizens. But they could do all of those good things for their citizens if they were non sovereign and dependent regional governments that were part of one federal government that ruled all the world. Sovereignty and independence is not needed for a government to do good for its citizens.
The main function of the sovereignty and independence of sovereign and independent national governments is to kill people in wars. Other functions of governments, less harmful and more beneficial, can be carried out by non sovereign and dependent local governments as well as by sovereign and independent national governments.
It is estimated that between about 16,000,000 and 30,000,000 people died in World War One, beside all the people wounded, and that about 56,125,162 to 85,000,000 people died in World War Two. So about 72,125,162 to 115,000,000 people died in the two biggest wars of the Twentieth Century, beside all the thousands and millions of people who died in smaller conflicts in that century.
So how many people will die in wars during the Twenty First Century (AD 2001-2100) because of the sovereign and independent national governments that exist today?
How many people will die in wars during the Third Millennium (AD 2001-3000) because of the sovereign and independent national governments that exist today?
How many people will die in wars during the ten thousand years that began with AD 2001 (AD 2001-12,000) because of the sovereign and independent national governments that exist today?
How many people will die in wars during the hundred thousand years that began with AD 2001 (AD 2001-102,000) because of the sovereign and independent national governments that exist today?
How many people will die in wars during the million years that began with AD 2001 (AD 2001-1,002,000) because of the sovereign and independent national governments that exist today?
Nobody knows, because the future is uncertain and will be the result of countless millions and billions and trillions of individual decisions which people will make in the future.
But imagine that a supernatural being gives you the power to decide whether separate sovereign and independent national governments will continue for as long as the human race survives, or a government ruling over all humans that live anywhere in the universe will be established immediately and last for as long as the human race survives.
What will happen if you choose in favor of the sovereign and independent national governments? Suppose that the future is more peaceful than the past, and only 1,000 to 100,000 people die in wars in an average year in the future for as long as the human species endures.
In each such unusually peaceful century, 100,000 to 10,000,000 people will die in wars.
In each such unusually peaceful thousand years, 1,000,000 to 100,000,000 people will die in wars.
In each such unusually peaceful ten thousand years, 10,000,000 to 1,000,000,000 people will die in wars.
In each such unusually peaceful hundred thousand years, 100,000,000 to 10,000,000,000 people will die in wars.
In each such unusually peaceful million years, 1,000,000,000 to 100,000,000,000 people will die in wars.
And beside the people who die in wars, many more people will be wounded, and/or will mourn friends and relatives who are killed, and/or will lose their property to wartime destruction.
And of course those calculations assume that the future will be significantly more peaceful on the average than the Twentieth Century.
So in my opinion, if your protagonist chooses to fight to establish separate sovereign and independent national governments in place of a world government, he is fighting for an evil cause. And maybe as a writer you can demonstrate to the readers that he is being misled by his patriotic impulses into fighting for the wrong cause.