We do. In the report from the above article, the arrest rate was similar for blacks vs. whites. If the arrest rate is similar but the stop rate is disproportionately larger that is a pretty strong suggestion that something is amiss.
Actually, if the arrest rate is similar it suggests that police are doing a fair job. It suggests that their estimate of "likelihood of being arrested" is equal across the two groups.
Consider alternatively that police stop many more men than women. Is that sexism?
Seriously, this is like problem numero uno with any discussion of racism. Racism doesn't always appear clothed in a pointy bedsheet.
As a white guy who tries to avoid assholes, I almost never see overt racism. When someone is overtly racist, it's almost always immediately addressed. That's a good thing! But it makes it super easy to think "Racism Is Over!" when that's your environment.