RFK is a true believer; he actually thinks, against all evidence and logic, that vaccines are bad for your health. Trump does not give a shit about vaccines, but he offered RFK the CDC position because A) RFK was running a third-party candidacy in 2024 that could have cost him several swing states and B) anti-vaxers are a large part of the Trump coalition, but he was losing their trust after promoting the covid vaccine. Most congressional Republicans are just going along with this out if cowardice.

So, tl:dr: ending vaccines is what RFK (stupidly) believes in, Trump put him in power to return a favor/appease a portion of his base, and every other Republican is too chicken-shit to do anything about it.