In the fairy-tales I'm familiar with, Baba Yaga doesn't exactly fly, but rather travels in a series of bounces, using the mortar and pestle as a sort of pogo-stick. She sits in the mortar and strikes the pestle against the ground with such might that the mortar (and herself) are propelled through the air for some distance. As the mortar falls to the ground, she strikes with the pestle again and thus does another hop. Sometimes she also has one or two birch brooms along with her -- skillfully sweeping the path before and behind the mortar even while she's simultaneously banging on the ground with the pestle.
She definitely travels this way in Василиса Прекрасная ("Vasilisa the Beautiful") -- certainly, illustrator Ivan Bilibin portrayed her crashing through the forest in what appears to be a levitating mortar (see above), in his pictures for "Vasilisa". And if memory serves, she also bounces around in her mortar to visit a wise talking frog, in the story Пойди туда, не знаю куда -- Принеси то, не знаю что ("Go I know not where, fetch I know not what").
But I'm not aware of any stories where the mortar and the witch are able to soar at great heights, like E.T. on the bicycle silhouetted against the moon.
On the other hand, there are a lot of stories where she never leaves her hut -- she just sits around and either threatens to gobble up the hero(ine), or on rare occasions, offers helpful advice about where to find some sort of magical item, like a character in a computer adventure game.
P.S. If I'm not mistaken, in the very earliest Superman comic books, Superman was also a "hopper/bouncer", like Baba Yaga -- he could leap a mile horizontally with a single running jump, or from ground level up to the top of a skyscraper -- yet he didn't actually fly. (Although it didn't take long before flying was added to the list of his super-powers.)