Irrespective of his intentions, or the quality of his work - which seem quite laudable, both his tremendous wealth and the political power of his foundation play into fears many have that the world will degenerate into an authoritarian, pseudo-technocratic plutocracy.
Capitalism and industrialization have made replaceable widgets of most workers. Many employers view their labor as expendable, reward incompetence, and exercise undue or (seemingly) arbitrary levels of control over how their employees live.
When the architects and winners of such dehumanizing systems, who wield power greater than that of many nations attempt to bypass traditional gates to power and directly influence public policy (especially policy concerning people's bodies) because they 'know' what's best, even with the purest of intentions, people have the right to be suspicious and concerned.
It also doesn't help that Gates seems to favor the diminishment of individual nations in favor of a stronger level of global governance. It's not popular with a lot of people, and on the fringes can even be taken as a form of soft treason.