There's two main parts, essentially.
First is that Ctrl+Alt+Del advertises itself as a comedic webcomic, when out of the blue it decided to have a serious arc culminating in the depiction of a miscarriage. People thought it was tone deaf and tasteless, and its inclusion in what is otherwise a lighthearted work of satire conveys the wrong message.
Second is related to the author himself, Tim Buckley. Tim has a reputation for being a bit of a scumbag, and it turns out this was an adaptation of an actual event that happened with an ex of his. In the arc, the woman depicted in Loss is being neglected by her boyfriend, who is Tim's self-insert character. Loss turns her loss into his loss, and the eventual lessons learned by the characters were how she wasn't prioritizing his needs enough.
Essentially, Tim turned a real-world tragedy for one woman into his own power fantasy, and he did so through a completely left-field turn in tone for his webcomic that left readers confused. So Loss became a meme, not because of the content itself, but because people wanted it to be something permanently associated to him and his comic that he couldn't just bury or move past.