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Because there's more factors to its popularity than just it's cuteness, which also aren't exclusively aimed at girls. Basically, it's also thanks to the evolution gimmick associated with it. More people like it as part of a set than by itself.
Remember back during Pokemania, it only had one episode in the anime dedicated to it, in that sense Pokemon like Psyduck eclipsed it.
It's well known in the games, however, being one of the original 151 and being the premiere split evolution Pokemon. It's rooted in nostalgia, yet also gets refreshed in people's minds every so often as more evolutions are added, naturally growing its popularity. That popularity osmosed, complete with autistic fan creations and even more autistic parodies that include shoving a stone up its butt. Some say its the prototypical sparkledog.
Then Nintendo took notice and started shilling it, just a little behind Lucario's level of shilling.
And then Sylveon was introduced, specifically targeting girls. Even then it served more than one purpose, being the poster child of a new type, an important milestone in Pokemon's history.
Then the bright idea of merchandise, like actual gemstone jewelry, specifically aimed at the adults who grew up with the franchise came along, and the ones with the Eevees have consistently sold out ever since. Now, girls (and boys) don't have to hide liking it for fear of looking childish or nerdy.
