They can just be friends y'know. In fact in this image that's what they are. Friends. Doctor to companion. Derpy might like him, but she doesn't get that in the way of them just being friends and hanging out :I
Derpy: Hold on Doctor! I'm bringing to my favorite cloud place.... Doctor: Hahaha! This is so much fun! It is the first time I fly that way... Are you okay Derpy? Derpy: Yes, Doctor! Are you enjoying it? Doctor: Yes! Pretty much! But, are you alright? Is it hard for you to pull it? Please.... don't strain yourself! Derpy: I'm okay Doctor! When I'm with you... I feel I could do everything.... Doctor: Still... promise me to not go over your limits.... okay? Derpy: I... I promise. Now, hold on... I'm going to make a looping.... Doctor: What?!? Don't you dare to.... ahhhhhhh!!!!