According to the Bureau of Justice Statistics [0], 52% of convicted felons in state prisons are there for a violent crime; 18% for property crimes; 18% for drug crimes; and 9% for public order crimes [1]. Violent crimes obviously harm someone. I would guess that property crimes and some of the public order crimes do as well---remember that we're talking about felony convictions, which means crimes that resulted in a sentence of one year or more. For the sake of discussion we'll suppose that drug crimes never harmed anyone. So a reasonable estimate would be that around 3/4 of prisoners in state prisons are there because they committed a real crime that actually harms someone.
Now obviously it's bad that 1/4 of prisoners are there for trivial reasons. In particular, we need to end the drug war. But you seem to think that the prisons are full of people who were caught with a speck of weed or who stole a loaf of bread to feed themselves, and that really isn't true. Minor crimes usually result in a fine, community service, or at most a few months in jail (which is not the same thing as prison). For the most part, people in prison are there because they did something genuinely bad. The original article mentioned one specific prisoner by name, an Adam Johnston; I found what I think is his record [3], and he's serving twenty years for murder.
[1] "Public order crimes" means "weapons, drunk driving, court offenses, commercialized vice, morals and decency offenses, liquor law violations, and other public-order offenses".
Violent offenders tend to serve longer sentences than others (expected to be ~3 times longer on average than most other categories, according to the BJS article you reference), which is part of the reason they make up such a large part of the prison population at any given time.
In terms of number of people sent to prison, they're less prominent: again from the BJS article, admissions to state prisons in 2009 with sentences >= 1 year broke down like this: 27% violent; 30% property; 29% drug; 14% public order; 1% other.
In this context we're talking about P(person did something bad|person is currently in state prison), so the relevant statistics are the ones I cited. Your statistics would be relevant if we were talking about P(person did something bad|person has ever been to state prison).
Now obviously it's bad that 1/4 of prisoners are there for trivial reasons. In particular, we need to end the drug war. But you seem to think that the prisons are full of people who were caught with a speck of weed or who stole a loaf of bread to feed themselves, and that really isn't true. Minor crimes usually result in a fine, community service, or at most a few months in jail (which is not the same thing as prison). For the most part, people in prison are there because they did something genuinely bad. The original article mentioned one specific prisoner by name, an Adam Johnston; I found what I think is his record [3], and he's serving twenty years for murder.
[0] https://www.bjs.gov/content/pub/pdf/p09.pdf
[1] "Public order crimes" means "weapons, drunk driving, court offenses, commercialized vice, morals and decency offenses, liquor law violations, and other public-order offenses".
[2] https://upload.wikimedia.org/wikipedia/commons/d/d3/Felony_S...
[3] http://www.drc.state.oh.us/OffenderSearch/details.aspx?id=A4...