Canonically, it’s some kind of pet store / animal shelter, so it’s probably donations and the occasional adoption fees. In Season 1, she was in charge of the Ponyville bunny census, which suggests she may have some sort of official position managing Ponyville’s non-domesticated wildlife (to the extent that any of Ponyville’s wildlife is non-domesticated).
The comic looks great, but I think the purple and red on Fluttershy and Rarity’s faces is a little too intense. It makes me feel like they might be coming down with something or they’re depressed or embarrassed