First, because they require more components. In an internal floppy, everything is controlled by the motherboard; the floppy drive itself is little more than a motor and a magnet. In an external floppy drive, all of the circuitry and control firmware that was part of the motherboard has to be duplicated. Then that data has to be converted to the interface that the external drive connects to (such as USB or parallel port).
Finally, the biggest reason is that they are a bit of a specialty device. Floppy disks aren't used very often any more, and computers often included floppy until way past their heyday, so it isn't hard to find a computer with an internal one.