Because planes flying long haul routes are larger than short haul route aircraft - for reasons of fuel ecconomy and passenger numbers. there is more leg room on a standard long haul flight aircraft, but if leg room is a serious issue for you, either for height or comfort reasons, you should discuss upgrading with your travel operator, who will advise the different leg-room dimensions available on various fare structures.
One of the US airlines - United? - has been promoting the fact that they have increased legroom -- a response to the collapse of their business after 9/11, I imagine.
One tends to get more room on schedule flights than on charters - i.e. a flight booked as part of a package deal. This tends to be reflected in the price - a schedule flight to to Florida - for example - can cost more than a complete package deal. Aircraft are configured differently depending on the operator so long-haul/short-haul has no direct impact upon legroom. Certain airlines have policies for allocating seats with extra legroom if one is greater than a certain height but this varies from carrier to carrier.