Yes, why blame the characters when the true fault lies with the creative forces behind the books?
Speaking of the mutant massacre, it was Destiny who advised Mystique to leave the tunnels. Freedom Force could have helped their fellow mutants, but bailed.
Thor was in the tunnels, battled the Marauders, saved Angel, and gave the slain Morlocks a Viking funeral. Leaving the dead bodies would have caused a health hazard.
Also, Thor has known the O5 since they were kids.
The Avengers also gave up their UN status to help out in Genosha.
It was the Avengers that destroyed the Mark II Sentinels.
The Avengers have legit history of being sympathetic towards the struggles of mutants.
When the X-Men were on reprint only status, the mutant saga was continued in various Marvel books.
I think the issue is creators being too territorial with characters & stories which gives the appearance of one franchise being apathetic with another.
Captain America can endorse tolerance for mutants all the live long day, and that will not stop forces from conspiring against them. Captain America & the FF have publicly endorsed Spider-Man, yet he has been historically viewed with suspicion (although it has been years since I read Spidey).