I think I've read the first issue, the start of the Chrysalis thing what with the "zombie" stuff at the start, and pretty much called it quits there. From what I've heard and seen about the storylines I'm really rather okay with that decision. However, one of the bigger turn-offs for me was the art style. I found it exaggerated the expressions way too much for my taste. Possibly because it reminds me of some of the more horrible faces the show proper has made at times.
The tone is also a problem for me. It just... doesn't quite feel the same to me. As some others mentioned like a month ago upthread it can be a bit darker, and it has a fuckton of references and nods. Like, way, way too much for me. Some here and there are cool, I guess, but... eeeeeeh.
If I want to read fanfiction I usually go to Fimfiction. Better stories, less hassle, up-front about the fact that it's fanfiction.
Whether or not you consider it canon is your own decision, but at least I think the tone is too different from the show, the team writing the comics isn't being watched over by the show team, and I find there to be too many inconsistencies to fit those worlds together.
All that said, if you enjoy the comics, I'm happy for you! Different people, different tastes.