How do some logia users fly?
Logia users, whose element is lighter than air, can fly by transforming (at least) their  lower body into that element:
Moku Moku no Mi (Smoke fruit)
Gasu Gasu no Mi (Gas fruit)
I am unsure if the Pika Pika no Mi (Light fruit) is based on the same or rather the special property of light.
I am not aware of other Logia users truly flying with their ability. They rather propel themselves into the air (e.g. Mera Mera no Mi / Fire fruit and Suna Suna no Mi / Sand fruit).
The Yuki Yuki no Mi (Snow fruit) can grant flight by creating wings made of snow but that is less of a Logia thing itself.