The low charter rate depends in part on spreading costs over a large number of people with virtually all of the seats being filled. Three hours is not unusual for an international charter. If a charter flight hasn't sold out shortly before departure, the operator can sell seats at bargain basement prices to latecomers. Some who have paid the regular price well in advance may object, but should realize that the operator's alternative may be to cancel the flight altogether for economic reasons. Ask your travel agent to compare fares on scheduled and charter flights for you.
Charters offer nonstop flights for an affordable price.
They can be a wise travel investment if you can be flexible in your travel plans. Just be sure you know the conditions for the trip you're buying before you pay for it.