I haven't looked at the different companies but there could be several factors.
Old plane vs new plane ... Speaks for itself
Location... Some parts of the country, aircraft rental just costs more
Simulator... Use of a simulator brings down costs a little typically
Part 61 vs Part 141... Part 141 utilizes a lot more dual training, so you are paying for an instructor on every flight.
If it is part 61, maybe they are adding the 50 hours x-country requirement to the course, but like I said I haven't looked at the websites