The article is a bit biased,just like most others coming from CNN,the reason being that they only report as hate crimes when minorities are targeted by the majority but not vice versa,which is much more common btw.While intolerance towards minorities in US in definitely on the rise,most of them are generally targeted by other minorities and generally Americans and immigrants alike, are far more likely to be attacked or killed by someone belonging to the minority groups.But in those cases you wont hear about "hate crimes",then the perpetrators are just suspects and the victims are just "at the wrong place at the wrong time".
As a European student who visited USA twice(second time having the misfortune to spend some time in Baltimore 2009) I know more about the subject then I would like to,but don't take my word for anything,ask any of the hundreds of thousands immigrants from ex Yugoslavia(mostly found in Atlanta,St.Louis,Chicago and Detroit)do they feel more threatened by the majority or minority groups.
The safety issues for everyone in some places in USA are really alarming and i don't see it getting better anytime soon,unfortunately.