What WaPo wants you to do here is assume that since black men account for 6% of the population, they only account for about 6% of total interactions with the police as well, which is false. That 40% number doesn't look so high once you realize that.
This is of course not to say that there isn't a problem with police shootings in this country. But the whole "lies, damn lies, and statistics" thing is highly relevant in articles like that.