"hurt the brand I love most in the world." And they often are. Whether you are a college fan or a pro fan, there is a sizable portion of *every* fanbase that believes the local beat writer unfairly attacks or criticizes their teams. Heck, in some markets people get death threats when they write negative stories about a team.
Fans feel a close connection to their teams and players, and the usual result is they will get defensive about anything that shows them in a negative light.
And yes, being a voice that sometimes covers issues that fans might seem as being "critical" or what you might think is a "pernicious brand of editorializing" is an indicator of good journalism. Being a good journalist often involves asking tough questions and covering sensitive topics or being in places that people think you are "snooping." It's a thankless but important job that keeps people honest while it also spotlights the positive in the community.
The sign of a good journalist is a person who can give voice to all sides of an issue, whether positive, indifferent or critical. Oftentimes, the best way to accomplish this is by giving voice to sources who may have opinions some people may not agree with. You also then do your best to give the organization voice. However, one of the difficult things about working in sports journalism is that often the people representing the organization do not respond as readily.
And "More positive?" Jay wrote plenty of positive articles about BYU athletes over the years. But bad things happen in all programs, even BYU. So he did his job and covered it and because he wasn't "rah-rah go BYU", some people are going to automatically think he's biased.