It isn't completely free, though. According to the estimate of his son, young Benjamin Sisko would have used up about a month's worth of 'transporter credits' during his first few Starfleet Academy days, just to get back to New Orleans to have dinner with his parents.
Or perhaps it is practically free, just not at Starfleet Academy, to teach those cadets dealing with limited resources.
Its probably free at the point of use for the general public (which likely also doesn't overuse transporters to such a high degree)... at SF Academy, this would probably be an equivalent to training exercise in dealing with limited resources.
The general public is probably also educated in school about how to use resources responsibly.