I think they are very, very afraid of being held 100% responsible for implementing the MAGA Murder Budget -- the most despised bill in my memory, and perhaps the most despised bill ever.
Trumpublicans are going to have a hell of a time getting appropriation bills that implement the abominable bill through their own conference, much less get the 60 votes needed to put those bills to a vote.
But they are loathe to get rid of the filibuster. They either want to be able to continue to blame Democrats when their appropriation bills stall. Or if they do manage to get any passed, they want to be able to say "if it were that bad, wouldn't the Democrats have stopped it?"
I also believe they are refusing to cave on the subsidies because it will set a precedent of doing their jobs and actually working with the minority party.
There is a reason that a functional majority party doesn't shove abominations like the MAGA Murder Budget down the throats of the minority. Sane members know that they will need the minority to IMPLEMENT provisions in an actual budget.
I think, one way or the other, they are going to be in chaos as the months go on. If they keep the filibuster, at best, they'll end up with a series of CR's funding at the current levels (each time having to cave on a new Democratic condition) and then be voted out.
If they get rid of the filibuster, they'll be unable to get their act together on key appropriation bills, pass a series of CR's on their own, and be voted out with 100% of the blame for whatever mess Trump makes.
Who knows. Thune may actually be looking to keep the filibuster so that, ultimately, the Democrats help them save themselves from themselves.