The issue was that it wasn’t really widely known at the time. Or at least, it was easier to handwave away as rumors and speculation. The church was still doing a pretty good job of keeping a lid on all their issues. So when she did it, all the Catholics immediately disregarded the protest and jumped on the “she hates God and Catholics” bandwagon. Some of the abuse was well known, but it wasn’t recognized to be anywhere near as pervasive and ubiquitous as it is these days.
She essentially made herself an easy target by not explicitly clarifying what she was protesting. Lots of people simply saw her ripping up the photo of the pope without any context as to why, so it was easy to take out of context.