If it involves flapping wings, and exercising muscles they yes. Telekinetic flight or superman like seemingly effortless flight then no.
However from a role playing perspective even if it was effortless I'd let them try, perhaps even let them think they are succeeding, until they realise they are sub-consciously hovering on the scales, and in reality they have put on weight. But then I am a RBDM.
I just flew in from Las Vegas, and boy are my arms tired!
But seriously, have you seen the food I get on those flights? Insects and seagulls!
I tell ya, smiling is a real bad idea on these trips.
Thank you, thank you, I'm here all week.
Try the veal.
I kind of differ in regards to telekinesis - if it burns energy, then yes, it can count as exercise. If he is wafting along, with no more effort than a thought, then no, he isn't exercising. (The image of him bringing his couch with him, reclining as he flies....

)
It all comes down to effort - in Wild Cards the Turtle does use energy to power flight and etc.. But for him it wouldn't be
exercise unless he was lifting battleships.... Much like I can't lose weight walking - I do it enough that my body has adapted. (Though
not walking would probably pack on the pounds.)
The Auld Grump, actually, I am glad to have some body fat, I no longer sink when trying to swim.