Though I only got to play along with the pro guitar trainer for a short time, every indication is that Harmonix has done exactly that. The guitar trainer is astounding -- paired up with the real guitar controller from Fender or the 102-button controller, Harmonix applies its steady knowledge of gaming reward and replay not just to earning career mode money or having fun with your friends, but to actually learning and applying a knowledge of chords and guitar notes.
The guitar trainer works very similarly to the keyboard trainer, and just like the other instruments, all of the music in this mode is original and designed just to teach the specific lessons Harmonix wants to teach (it crosses all sorts of genres as well -- you'll have to listen in to one of the tracks for a mandolin). Of course, it's meant to work only with the full guitar controllers, but you essentially play the trainer like a game, hitting the various rows of notes that come at you, all while notes and text on the sidebar teach you about the chords and notes that you're playing.
At its most basic, the trainer is meant to simply get you to play the songs in the game -- the patterns and runs you're taught are the same used in the actual note charts of each song. But the game also points out where you're learning real guitar notes and moves, and eventually, as you learn to "play" the real guitar along with the Rock Band songs, you'll be able to play it outside of the game and churn out a recognizable riff. In the trainer, you'll learn to play a series of chords, which will help you play along with the note patterns in "Crazy Train," and then when you walk away from the game, playing the same notes will get you a tune (though probably not the actual song) that sounds enough like "Crazy Train" for other people to recognize it.
The trainer is very forgiving -- if you miss a note, it will allow you to go back and start over, and you can adjust the speed as you play, or even add a metronome if you need it. You can repeat lessons anytime you want, if there's one you specifically want to practice.
I also got to play with the full Fender guitar and, as you'd imagine, it's a quality axe -- full-sized, with real strings and buttons compatible with all of the consoles (so you don't need to buy one specifically for each system). There's a muting toggle on the strings, so you can pull it up to just play along with the game, or press it back down if you want the guitar to ring out. Personally, I'm only accustomed to the feel of an acoustic guitar, but the Rock Band Fender seemed to me like a standard size and weight for an electric model. Our sister site Engadget has a more in-depth look at the guitar itself, from both an actual guitarist and a hero of the five button frets.
Harmonix said before that what it wanted to do with Rock Band 3 was take on the naysayers who said you couldn't learn real guitar from a music game. After playing around with the guitar trainer for only a little while, it certainly seems that with a enough time and practice, this game will actually have you well on your way to becoming just as good at the real thing as you are with the plastic axe.