There's playing by ear...and then there's playing by ear. ;)

Hearing a song and playing along with the chord progression is one level, IMO. Hearing notes/chords and identifying them is another level. Hearing a song and playing the lead or melody is yet another.

It never came to me naturally when I was a kid taking lessons. And although I knew about I - IV - V progressions I never 'heard' it in a song until two or three years after I stopped taking lessons and doing daily practice. Sitting in my college dorm room one afternoon, I 'heard' the progression in a record on the radio and that ah-ha moment allowed me to hear and play progressions for the rest of the time I played guitar (I have come back to guitar after a decades-long break). But my skill level is not up to playing melody/lead by ear...yet.

The breakthrough song? Interestingly it was already an oldie when I heard it that day -- "Shiela" by Tommy Roe. :D

I suspect with GT lessons and scale practice that the other level of playing by ear isn't too far down the road for me. After all, all it takes is technique and an 'ear.' Then again, I'm not experienced enough to know if I'm wrong. ;)

FYI, GT has some ear training resources and there's bunches on the 'net including iPhone/Touch/Pad apps.