Illinois Terminal; Chicago, South Shore & South Bend; and Pacific Electric all had freight operations similar to line-haul "steam" railroads. Others, more like trolley lines, were Chicago, North Shore & Milwaukee (and arguably that could belong in the first category); various lines in Indiana which were later merged to form the Indiana Railroad; I think both the Cedar Rapids & Iowa City and the Waterloo, Cedar Falls & Northern, both in Iowa, had freight service. There were plenty more in many parts of the country which probably had some sort of freight service but I can't say for certain. I'm sure you'll be hearing from others who can add some names to the list. As a parenthetical note, the Chicago, North Shore & Milwaukee had TOFC (piggyback) service back in the day.