No, it really is the way you're writing about it.  

Some of the problems are just basic bad journalism, like relying on secondary sources, many of which lack credibility, like blogs and social media.  You don't seem to make much, if any, effort to follow up on these sources and make sure they're accurate or get different perspectives on incidents.

The primary issue with this piece is that you've created the appearance of an association between a white supremacist blog and the restaurant.  Even with the edits, by using the blog as an exemplar of those supporting the restaurant, the clear implication of the piece is to say that someone who supports the restaurant is a white supremacist.

It's hack journalism.  It's unprofessional.  It's propaganda dressed as news.  Worse, in its deceitful muckraking capacity encouraging the protests, it's demagoguery.

Should be good on your CV if you apply for a job with a sleazy politician, though.