I think Gates' point is that government is an important part of the solution [to R&D, and to climate change]. The founder of Microsoft is not saying there is no role for private R&D.
The point is that the private sector is going to focus on exploiting hydrocarbons until green energy becomes more economical by comparison. But the planet can't wait that long.
It's also a self-fulfilling prophesy: the private sector won't invest in green energy until the returns vs. the risks are sufficiently attractive compared to investing in the exploitation of more hydrocarbons. But that won't happen until more is invested in green energy. Govt. can kick-start the process of making green energy an attractive investment and then let the private sector run with it.
Governments have the ability to make the kind of investments that the private sector generally can't, namely the kind which payoff in intangible ways, not strictly profit. Think of the graduate student who learns skills which are otherwise difficult to come by, while pursuing a science degree doing fundamental research funded by the National Science Foundation, for example, then goes off and applies those skills in the private sector. Think of the government lab which sells time to anyone who want to use some large, complicated, expensive instrument. Can a startup company afford to buy an electron microscope? No, but maybe they can afford to rent time on one at a govt. lab which charges at cost.
Think of the mapping of the human genome. Think of all the undergraduate students who benefit from learning from so many scientists whose research is funded by NASA, the NSH, NSF, DOD, DOE .... On and on.
I don't know how government R&D worked in the USSR, but I suspect there are two key differences. (1) The US capitalist economy generates more tax revenue which allows more government funding for R&D. (2) The US system of funding R&D is based on competition and peer review, and actually the way the National Science Foundation and other agencies determine who/how much $ to grant, is somewhat similar to venture capital. Scientists competing for these grants are not like the 9 to 5 worker at the DMV just taking a paycheck from the government and counting down the days until retirement, it's very vibrant and dynamic and rewards the best scientific entrepreneurs.
The third thing I would add is that unlike a Communist country, in the U.S. once the basic research is done the private sector is left to run with it, make it commercially viable and produce and distribute products on a wider scale. Gates isn't saying we should be a Communist country, he's saying we should be a Capitalist country with a strong government R&D program.
The main difference between the NSF and venture capital, of course, is that while both take into account the costs and the risks, the govt. doesn't measure returns in dollars but by the intangible (yet well-defined) metrics of how the research will further the NSF's stated goals. Of course, those intangible benefits do turn into dollars for society ultimately. But that occurs by innumerable and circuitous ways, and the benefits don't accrue to the investor directly (I.e. To the govt.) but to many people indirectly (the students who spend a summer in the lab, the private company that uses the research to commercialize a technology, etc.)