The system is a byproduct of reality as well as perception, while I am sure there are people within the system (historically) that have manipulated its implementation to serve their own particular agenda's, it is often simply 'cause and effect'. At some point, there was a necessity to treat various members of society somewhat differently, whether this registers as 'right or wrong' is irrelevant, I am merely highlighting the concept.... As a direct consequence programs were implemented to tackle what the public perceived as being a 'threat'. The notion of 'racial discrimination' is intertwined with socio economic status, more crime is inherently found in lower income areas where the socio economic status of its inhabitants lend themselves to criminality. As stated in a previous post, the reason why the vast majority of these poverty stricken areas are made up of minorities is open to debate, however, it is a fact never the less. Ergo, if crime is associated with lower income areas and the vast majority of these low income areas are populated by Black Americans, Latino American's etc... then the logical association (think Pavlov's dog's Classical Conditioning) between Crime and Ethnicity is positively reinforced. Again, this isn't an endorsement, but it does set a level of context that is often overlooked.
Does this mean the system is 'racist'? Perhaps depending on your perspective, however, it is important to acknowledge that there is a reason it exists.... cause and effect.
This is an interesting grouping of statistics compiled by the BJS, shows some of the issues faced, but it also shows disparities between genders and other variables that are consistent with the same psychological and physiological profiling methods as highlighted above:
This article is a little longer, but it's definitely worth a read irrespective of your personal stance:
http://www.amren.com/archives/reports/the-color-of-crime-2016-revised-edition/
Some additional statistical figures for reference:
http://www.bjs.gov/index.cfm?ty=tp&tid=702
Here is another table of statistics showing various ethnicities and arrests:
https://ucr.fbi.gov/crime-in-the-u.s/2013/crime-in-the-u.s.-2013/tables/table-43
No one is suggesting that 'Stereotypes' are fundamentally true, however, there is a reason that a Stereotype exists, it is loosely based upon experiences albeit subjective and dated for the most part. With that knowledge though, people are often subject to 'Stereotype Threat' whereby they subconsciously fulfill the said stereotype as it is an expected action.... you can see where this becomes a vicious circle though, as a non accurate stereotype is positively reinforced by those observing and thus creating the illusion that it is both accurate and true.
A good little video from a Stanford Professor on Stereotype Threat (and this isn't simply based around Race:
While i do agree with the notion that people shouldn't be pulled over based upon 'race' alone, it is simply impossible to remove it from the equation. If I am looking for a radical insurgent with ties to ISIS, then the ethnicity, gender and physical appearance are fundamentally important. This is profiling of course, but in the role and context of its application it is almost impossible for it to be removed... and nor should it in this case.
The real issues may appear to be racial in nature on the surface, but when you look a little deeper they are more intertwined with economical status and poverty.... and that is an entirely different discussion!