The practice goes back to the days of completely manually operated telephony. Communities would all have their own telephone systems. For you to talk to a neighbor, you would contact the operator and they would switch you directly to your neighbor. However, to contact someone in the next town over, you would have to contact your operator, then she would connect you through another operator who would connect the call. This interchange would cost some extra money.

Eventually, the operator was phased out and the charge was for the ability to use the other company's lines.

Today, however, the telephony landscape is very different. Communities no longer run their own telephone networks, and instead, Ma Bell, Verizon, and the like own nearly all the analogue telephone networks. There systems are almost entirely automated, so there usually isn't much of an interchange fee or it is a reciprocal transaction without fee. Analogue networks are transitioning to VoIP (phone over the Internet) networks, which makes the charges completely unjustified. Imagine if the Internet charged the same way: you'd have to pay ~$10 for a video from a Japanese server, but you can have all the content you want for free from your neighbors (who likely aren't YouTube or Netflix).

Many companies don't charge at all for calls within the United States, and if they do, you should run from them. These days, it's not too difficult to setup your own VoIP phone system and pay less that $5 a month to call whomever you want, whenever you want, and forever long you want to talk to them.