NPR has a clear political agenda biased toward a particular party. While I happen to agree with a lot of their politics, I don't think organizations with political agendas should receive public funding. Also, the bulk of their funding is not from the government, so they should do fine. Musk is not pushing for something crazy with this.
One other problem with NPR is that they also take money from some seriously questionable orgs, like Walmart and McDonald Douglas.