What could I do to help my players feel like their choices matter?

[DeTess]

I agree with what most of SaintHeart said. However, there is something else that you might want to consider, OP. Where the players aware that taking the Doctor with them was a True choice? If I was playing in an adventure, and at the end of a dungeon I'd find some gold and other loot, and this doctor-dude (and nothing else plot-related), I'd kinda assume that he doctor is a plot-coupon that we need to interact with to further the adventure, and any choice related to leaving him behind or not being a false choice with only one right answer.

I don't know a lot about your campaign, so I don't know whether this was the case or not, but it might be worthwhile to ask your players if they understood that leaving the doctor behind was a completely valid choice.