I'm assuming because the majority of uses of Pepe the Frog have been, and continue to be, non-bigoted. However, it was inevitable that, as the meme proliferated in on-line venues such as 4chan, 8chan, and Reddit, which have many users who delight in creating racist memes and imagery, a subset of Pepe memes would come into existence that centered on racist, anti-Semitic or other bigoted themes.
But I don't see why they don't make it case basis like Forrest said. Stupid.