Most of the angst is just insecurity on BYU fans' part: "He doesn't love us like we thought he did! He didn't say how special we are!"
We fans love BYU for many reasons and many of us have a ton of history with the school. Many of us (of course, not all) grew up as fans, wanted to attend there, ultimately attended there, maybe met a spouse there, and have other family members who share that passion. I don't think Pope was lying when he talked about the special things about BYU. I think he valued them due to his connection through the Church. But from a sports and fan perspective, his alma mater is where his heart is. OK, that's fine. Do we really need the validation from him that would come with a farewell message about how amazing BYU is? I'll admit that, to me, not doing that seems a bit out of character for Pope — but if we can't feel good about things without the validation of someone who just moved on, our fandom isn't very strong.
I think he did good things while he was here and now we're turning a page. But chill out on the drama.