For one thing a large commercial roof will tend to have large air conditioning units on it that have to be contended with and if it is, for instance, a restaurant this can also make a difference, because they will tend to have more mechanical features on the roof. These can drive the cost up significantly, because they often have to be lifted by a crane to be roofed under and around.
However; if it is a warehouse roof with no mechanical features on it, it will make a big difference in the price. New roofing products are now being used that were specifically designed for commercial roofing, such as torch down rubberized roofing that are fast replacing conventional layered hot roofing, so there are now more choices in roofing materials to choose from when having a commercial building re roofed.
What type of products you choose can make a huge difference in the cost of a commercial roofing job, so it is important to bear this in mind. Also, it is important that you choose a roofing contractor that does roofing on a regular basis, as they will tend to have the manpower and the equipment that is required for a commercial roofing job.
What will ultimately determine the total cost on a commercial roofing job is the square footage, so it helps to pre-measure the roof so you know the amount of roof that you are dealing with when you are in the process of taking bids.