I also heard this caller today and was not totally satisfied that Neal answered his question adequately.
The caller's argument was that he had alsready paid his INCOME taxes on the money he had invested in his Roth and that under the Fair Tax he would essentially be paying that same income tax when he spent the money. Those people who have taken advantage of the traditional, or "tax-deferred", IRA's would not be paying that double INCOME tax.
The Fair answer to the caller's question is: Yes unfortunately under the oppressive income tax system we suffer, some forms of tax relief were conceived to allow people to plan for their retirement in a tax advantageous way. This plan does not address those concerns.
I think this is one of the transitional consequences and will be a tough sell to those, like myself, who have invested at least some money in Roth's.
But remember that if the "protected" money under the present system, just about as much will be taxed in the form of higher prices caused by the tax system that we pay right now.
That isn't a huge difference, but with the FairTax you can accumulate savings and investments and not be taxed until you spend (your choice) on taxable items. That's a big difference.