It’s probably because they’re pretty boring together, actually… their friendship mostly seems to consist of Rarity liking to talk about herself and Fluttershy being sweet and quiet enough to always listen patiently. Fluttershy has better chemistry with Pinkie and Dash IMO because they put her outside her comfort zone, and Rarity plays off Applejack and Pinkie well.
We need more interaction with these two. During season 1 they were together all the time, with Pinkie and Dash hanging out with each other. In season 2 it seems they switched, with Dash spending time with Fluttershy and Pinkie with Rarity.