Trump clearly doesn't like Thune and has said multiple times he wants him primaried and will endorse a challenger. So far no serious primary opposition to Thune has emerged.
Will someone else enter the race? Will Thune lose?
Yes and no. Almost certainly some obscura while challenge Thune, and even more certainly they'll lose in a landslide. Thune has done nothing to antagonize the MAGA base except perhaps not joining the Sedition Caucus, and I don't think the base will be too angry with him over it. Unless Trump endorses Thune's challenger, in which case the race is probably between Lean and Likely Challenger, the race is Safe Thune. Given what you said in the first sentence, it's quite likely the former scenario becomes reality. I think some of Trump's comments may be talk - he might dislike Thune but I doubt he has some burning vendetta against him the way he hate the 17 GOP members of congress who voted to impeach/convict him. So right now I'd say Thune is favoured to win, but if Trump makes an endorsement (as I said, quite possible but not that likely), then Trump's endorsee has the edge.