'Package' holidays came along when tour operators realised that they could get round the rules, which banned other airlines from operating on these routes, by chartering their own aircraft for the exclusive use of customers who were booking their inclusive holidays. These tour operators then found that they had spare seats on many flights which they wanted to sell to the general public but they were prohibited from doing so because this would turn the flight into an unauthorised scheduled service. To get round this they sold 'flight only' tickets which (in theory, at least) also included accommodation so that they were still, legally, selling inclusive holidays. This meant that anyone who purchased a 'flight only' ticket also received a voucher that entitled them to use some sort of accommodation. This would probably be a bed in a grubby hostel many miles from the airport (from which there was no transport) and hardly anybody ever tried to use the accommodation. All the same, the tour company still had to make the offer of accommodation, just to keep the flight 'legal'.
With the de-regulation of Europe's airlines, companies are now free to operate on whichever routes they like and the rule about the provision of accommodation for charter flights has become obsolete (and been abolished).
Charter flights are still flights where the aircraft has been chartered by a tour company, mainly for the use of customers on inclusive holidays, but the person who buys a 'flight only' ticket on one of these planes will not really notice any difference between the two types of flight.
Chris