I believe you need one of the input devices (iRig; Ampkit Link; Apogee etc) to do this.
Someone will no doubt correct me if I am wrong
The interface connects to iPhone/iPad/iPod touch via 1/8-inch cable, automatically detected by iOS & has 1/4-inch mono input jack for electric guitar, bass, and line level signal sources and a 1/8-inch stereo output jack for connecting headphones, powered speaker, or PA system
Good news is that they can be bought relatively cheaply and will work with ipad and a number of applications such as Amplitube, GuitarToolkit and Ampkit...
Okay, but why Apple does not say? It just says to connect the guitar to the jack.
What you say may be true but it does not seem a detail implied.
Would suffice to say "connect your guitar with a special connector."
I think there should be a different solution.
If this were so, that we need a connector as IRIG, it would be annoying because even here: http://support.apple.com/kb/TS3698 not give the irig or similar solution but two tricks really unnecessary
When you plug something into the headphone jack, the speakers are THEN muted. Thus you can't hear out the speakers, it thinks you have headphones plugged in. With a devices such as Apogee or iRig, which I have, it provides a place to plug headpones in. I hear no sound out the speakers when I have ANYTHING plugged into the headphone jack. SO it makes since to me that you would't hear anything, the ipod thinks its headphones.
May I ask HOW you have your guitar plugged into the ipod? Via a regular guitar cable, then plugged into some short of adaptor for mini headphone jack?