At The American Scene, there's a short post about the two worst children's books ever, The Giving Tree being one of them. Shel Silverstein's mom (or someone pretending to be his mom) left a vigorous defense of the book in the comments, which included this statement: "It would be absurd if a fully grown and completely developed adult human being loved a plant." As one who speaks to precious plants in baby talk, and has been known to snivel when they "pass" to the compost heap, I know where that puts me. But if that's the attitude to plants his mother taught him, it's no wonder he wrote the book he did.
So, what children's books are there where plants are loved? The Secret Garden is the only one that comes to my mind-my favorite part of the book is the bit where Mary clears the encouraging vegetation away from the shoots of the bulbs. And An Episode of Sparrows, by Rumer Godden. Oh, and The Little Prince.