first of all, if the sub is designed as a home theater sub, it should be magnetically shielded (as are all speakers used in home theater setups). This is unless you are using a loudspeaker/PA system speakers, which are usually not shielded. I have 3 7.1 systems in my house, and all of them have the subs within a foot or two of largescreen HD sets, and no probs with any of them.
most subs used in home theater systems are 10" or smaller, most home theater in a box subs are around 6.5" which would not have a very powerful magnet at all, and i doubt it would fry your ipod.
I have a sub in my car that has a HUGE magnet, HUGE, as in the freaking sub came in a wooden shipping crate, and weighs over 50lbs, and its sitting within a foot of several different "brain" units for my car audio system, and the gigantic magnet in the sub hasnt caused one issue with the equipment in the trunk.
i am willing to bet that the sub had zero to do with it, just a weird coincidence.