Why do the children use the flowers while flying?

Mrs. Whatsit gives the children flowers for them to breathe through as they fly higher and higher into the rarefied atmosphere of Uriel. The children fly over an Edenic garden in which beautiful creatures dance to music; no wonder that Meg finds it so blissful.
Here, as elsewhere in chapter 4, nature is presented as a source of joy and wonder, a much-needed antidote to the infinite darkness of the Black Thing. That the children can breathe through the flowers indicates that nature is a source of life, a precious gift given to us by the Almighty. Just as flowers represent a thriving habitat for countless birds and insects, they also allow the children to maintain a connection to the earth far beneath them while enjoying a God's-eye perspective on things.

In this scene, Meg, Calvin, and Charles Wallace have arrived at the planet Uriel with Mrs. Who, Mrs. Which, and Mrs. Whatsit. Mrs. Whatsit gives them each a flower shaped like a bell with many little flowerets inside. They each use their flower to breathe oxygen when Mrs. Whatsit carries them up out of Uriel's atmosphere. The flowers function much like an oxygen mask on an airplane.
Mrs. Whatsit takes them up close to Uriel's moon so that they can see the dark Thing that obscures the planet Camazotz. They can't perceive the dark Thing while on Uriel, because the atmosphere hides it. They also can't see through the dark Thing to find out where their father is, much as they would like to. Mrs. Whatsit has allowed them to view the evil force covering the planet so that they will have some idea of what they are up against. They will have to discover their father's location on their own.