Multitrack recorders allow for the recording of a limited number of channels, or tracks, usually no more than eight or ten. With a computer program such as Pro Tools, the number of tracks is limited only by the speed of your computer's processor and hard drive.
Multitrack recorders usually have on-board displays, but they are no larger than 3 or 4 inches, and display limited information. A user of Pro Tools, however, has access to significantly larger monitors, allowing the display of more information at one time.
Multitrack recorders have smaller hard drives than one would use with a program such as Pro Tools. Larger hard drives allows more music to be recorded.
You'll be able to process your recorded music with a multitrack recorder, but you probably won't have as many options as you would with Pro Tools. For example, Pro Tools users have available a number of "plug ins" that can be used for pitch correction, which are not available on multitrack recorders.
If you want to master your recording prior to having it replicated, Pro Tools offers more sophisticated tools than do most multitrack recorders.