Dzarda has it right. The prototype-type PCB fabrication places will send you printed circuit boards, and that's it. These boards are suitable to test your circuit, and can be used for very small production runs if you have the ability to populate them. They can be used for HAND ASSEMBLY of your circuit. They will generally not be suitable for an automated assembly process. Thus, if you buy the PCBs and send them to an assembler, you will get charged for circuit components (with a handling fee tagged on, which can range from about 10% to silly levels), plus estimated technician time for hand assembly. You may also have NRE's tagged on -- a "non-repeating engineering" fee. This can actually be pretty reasonable, all things considered, especially if the company you're working with deals with non-domestic assemblers of good repute.
That said, to bring your product up to a manufacturable state for automated system, you might even find yourself paying MORE per PCB than you do at your prototype supplier-- sometimes just because your order comes in at less than the minimum price for PCBs. Also, pick-and-place assembly fee schedules can be surprisingly expensive for small production runs. Avoid doing anything silly, like mixing SMT and through hole parts, or having components on both sides, unless you're willing to pay for the adding processing.