FujiFilm S2800HD has a 14.0MP 1/2.3-inch (6.17 x 4.55 mm ) sized CCD sensor . On the other hand, Pentax 645D has a 40.0MP Medium format (44 x 33 mm ) sized CCD sensor and features Prime II processor.
Pentax 645D's sensor provides 26MP more than FujiFilm S2800HD's sensor, which gives a significant advantage in real life. You can print your images larger or crop more freely.
On the other hand, please keep in mind that Max sensor resolution is not the only determinant of resolving power. Factors such as the optical elements, low pass filter, pixel size and sensor technology also affects the final resolution of the captured image.
One other difference between these two cameras that is worth mentioning is that Pentax 645D's sensor doesn't have an anti-alias (Low-Pass) filter. Removing anti-alias filter increases the sharpness and level of detail but at the same time, it increases the chance of moire occurring in certain scenes.
Below you can see the S2800HD and 645D sensor size comparison.
As seen above, Pentax 645D has a 51.7x Larger sensor area than FujiFilm S2800HD. Larger sensors give photographer more control on the depth of field and blurry background compared to smaller sensor when shot in same focal length and aperture.