Probably the actual origin of this quote, or at least the inspiration for it, is a poem by Ella Wheeler Wilcox (1850-1919), who (it should be noted) died long before the first Pooh book was published. In her poem 'The Weed', published in "Poems of Progress and New Thought Pastels" (1911; London: Gay & Hancock), she wrote: "A weed is but an unloved flower!".
Interestingly, however, even the Texas Education Agency thinks this is a quote from Milne, including it as the subject of a essay question in the State of Texas Assessments of Academic Readiness exam for English Writing, raising questions about whether people at the Texas Education Agency quote Milne without reading any. Naughty.