The answer is really dependant on what type of operation your running, the conditions, and how you're going to be using the iPad. Also what type of avionics you're using.
Please provide a little more information...
I am really interested about what you see as the relevant conditions. The ones I can think of offhand:
1. Using the GPS functionality for primary navigation: That piece would be no different than for any other noncertified GPS installation
But that's not what the OP is asking; sounds to me that we're only talking about the type of media used for the charts. For example, you don't really need GPS to use the charts on an iPad - you can go to and bring up the ones you need just like with paper (although using less space and in theory quicker). In that case, whai I think wouold count:
2. Is is Part 121, 135 - Regardless of whether it's "really" OK, in the absense of an overall regulatory blessing, probably needs to be dealt with in OpSpecs. Without guidance from the FAA as a whole, whether you are going to have a problem with it will depend on who investigates. Might as well get the nay or ok up front.
3. Is it Part 91. For non Part F ops, where charts are not a requilatory requirement? The chances are it's ok to toss the paper and use the electronics, subject to the usual warnings about id somehting goes wrong, there's going to be more ecrutiny over the unusual than the usual.
4. Is it Subpart F, where charts are required? Id like to say what I said before - charts are charts. But at least having a set of paper charts on board as a backup is pretty cheap insurace against a potential enforcement action.
What other considerations do you see and how do you think they weigh in on the issue?