Actually, you're jumbling several things together here.First, Automatic Train Stop (ATS) usually uses wayside magnets that energize when a signal is red. If a train passes, the magnet pulls open a valve that dumps the train air. This technology dates to the 1920s.
Second is Positive (not passive) Train Control. This is a system that consists of a GPS receiver on the loco, an on-board computer, and digital radio links to a central office. Central office grants movement authorities digitally; as train approaches authority limits, engineer is warned and then brakes are applied to stop the train short of the authority limit. This system may or may not be "overlaid" on existing signal systems. Tests are underway in Illinois and Michigan (Amtrak), South Carolina (CSX), and on BNSF.
Finally, the "scanner" you mention is part of a system of Automatic Equipment Identification (AEI). Freight cars have passive tags that are interrogated by microwave as trains pass the reader. The information (which consists only of car numbers) is passed to the railroad's train consisting software to be checked against the recorded consist.
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