The raw material price is just an estimate on how much you would need to pay for the raw materials used for making the ship. Keep in mind, this is raw material only. Then, you have to have a datacard, which is used to produce said entity inside of a shipyard or other equivalent facility. All of this has to take place in a facility, bare in mind, and is therefore owned by a faction or rich person. Sometimes these facilities are rented out for production purposes, in which case some sort of monetary benefits must directly ensue. All of this and the fact that profits must be made afterward lend in the fact that prices might seem so steep.
Think of it more simply like this. In real life, Apple is a booming company known for their MP3 players, the iPod. Now, an iPod's production cost is pretty low for the company, as well as shipping and packaging, yet they sell for upwards of $300. This is because like Combine, everyone's in it for the money and it's basically what turns the world round.
Hope that helped!