I think Rubio would question him- not in public of course. Rubio is potentially going to have the worst time with Trump. Rubio is deeply knowledgeable about foreign policy. He's thought about it. He can speak on it deeply and intelligently. He can speak with an educated mind on most countries in the world. He has a much deeper level of understanding than Trump does- and every "envoy" Trump has appointed. So that can easily be a real problem.
Rubio (like Mayor Pete in Biden's cabinet) also knows he has a possible future in politics- maybe for decades. Trump doesn't. Rubio knows this and he won't go down with Trump if Trump does something crazy like kisses Putin's ass.
There are many reasons, but Trump has already appointed some other people to be "envoys" for the state department- a few of which Rubio doesn't see eye to eye with.
I think Lee Zeldin would push back against Trump- in private- if necessary. Zeldin would love to run for governor again in New York and he can't win as a Trump right winger. He'd have to be seen as slightly moderate on some positions. He knows that.
There are several others in that category.
For some, this will be the last government job they ever have because I don't think most will be viable options after serving in the Trump administration. (same is true for some of Biden's picks) Just look how many officials in the 1st administration aren't around anymore- and even have had trouble getting jobs in the private sector in some cases.