"Being uncomfortable around Police does not mean a person is a criminal, a bum or a bad person."

But it's a dang good indicator! I mean really afraid to the point you'd get up and leave the store because they came in?
Maybe a Cop told you your parents died in a car crash and you were forever fearful of seeing them. OK, not a bad person. That's a thin exception. As are most of the things you could come up with to support your point.

"Are most Officers good?... Yes. Are there some that have shown they can abuse the power given to them by their job?... Yes. Do the good Cops make the news?... Rarely."

For some of the Bad Cops DWB is still an offense, and that rightfully makes people nervous. Not the problem of the barista in a Starbucks to solve. I've been screwed over by the cops more times than they've helped me. Had them LIE in police reports, given me tickets for something I didn't do. Blah Yada Blah. The cops have saved me a few times too, after robberies. Let me off with warnings for traffic violations (about 50-50) Still, with all of my negative encounters with cops, I'm not afraid of them, and overall I support the job they do.
Your average criminal types ARE afraid of cops. Maybe "afraid" is too strong a word. "Mindful" "Uncomfortable" Etc.

"Combine all that with the fact that Officer involved shootings increased 100% in that area over the course of last year, to a number greater than that or either New York or LA, and I can understand why some good people could feel uneasy around Police officers around that town."

I won't ask you for Damned Lies (statistics) in support of this, but again: Good People don't feel so "uneasy" around cops that they'd avoid a business that cops frequent.

"The employee was put in a tough spot especially considering that every employee was put through "sensitivity training" last year. I don't think they handled it well, but I don't think the Police Officers Association needs to take their hurt feelings to Twitter either."

Employee in a tough spot? Yeah, being too stupid to hold a job in a decent business. I've fired people on the spot that had worked for my family for years for saying inappropriate things to a customer. This didn't need to to go Starbucks corporate, just the shift manager on duty. Then maybe if the cops had seen the proper thing having been done, we'd have heard nothing more about it.
Hurt feelings to twitter? Really? Everybody else can, but it's wrong for the cops to do so when they've been slighted?

I ask that you give some serious thought to your disagreement.