"Fluttershy is a tree" is a phrase that became a meme. It is usually used when telling someone that Fluttershy IS, in fact, a tree. Several renditions of her being a tree have been seen, and sometimes she is shipped with Bloomberg, Applejack's tree she is moving to her cousin's orchard. Or Tom, the rock that Rarity became obsessed with for awhile. The Fluttertree is often shown as an oak with pink leaves and yellow bark. This X is a Y meme is also used in reverse to call trees Fluttershy.
The idea that Fluttershy is a tree came from the twenty-first episode of the first season of My Little Pony:Friendship Is Magic, "Over a Barrel". Where in one scene, Pinkie Pie and Rainbow Dash were whispering to each other discussing whether they'd have to carry a tree, out of the train. Pinkie Pie then asks if she were referring to Bloomberg, the tree, in which Rainbow sarcastically replies, "No, Fluttershy." This sparked an argument between Pinkie, not getting the remark, whether Fluttershy is a tree. This ruckus causes a visit from Twilight Sparkle, who had just awaken. After all this hub-bub, Fluttershy then comes in saying "I'd like to be a tree." Thus the meme was born and will forever live on forever as a tree. Implying A tree can into pony.