The problem, I think and the reason why it is often mentioned that Jogan is toxic is for people who say it is harmless and it was not bad just because Jean never got to sleep with Logan.
Almost everyone recognizes that Scemma was toxic and pure lust, that has parallels with Jogan that Emma really loved Scott, while while Scott could love her it was never as much as Jean, if not, he would not have broken up with her the way that did him. The same with Jogan, Logan loves Jean, Jean can get to love him but it can hardly be a real love like the one she has for Scott.
Certainly another reason why Jogan is often mentioned is that unlike Scemma Jogan has been strongly represented in the media, even assuming that Jean can get to love Logan more than Scott, Scemma on the other hand has not had this type of representation, in WaTX what Scott may have felt for Emma was completely eclipsed by the love he had for Jean.
Scott never stopped loving Jean, maybe some writers wrote him at certain times wrong to make Scemma look better, but in the end we know that Scott never forgot her, he always loved her and Emma knew it but still followed him.
Scott did bad things, that nobody is going to deny, but Jean was not a perfect wife either, "Saint Jean" is usually used by fans who want to ignore all the mistakes of her and the haters who hate her. Besides maybe it is not canon, but in many AU Jean cheats on Scott with Logan, things like these have created the false idea that Jean loved Logan as much or even more than Scott, so maybe it never really happened in the canon but Jogan is much better known than Scemma.
The world is never black and white (good and bad) there are only grays.