I'm not expert on this, but have read boards where the experts post...
My understanding is that cellphones can still cause interference with navigational systems and cockpit instruments. Not all phones, not all planes. But in the right random coincidence of circumstances, it can happen.
Obviously, if the pilot is on the phone and simultaneously gets weird cockpit info, s/he knows what's caused it. Similarly, on a small business charter, s/he can quickly establish whether the cockpit info is correct, or it's just a client on the phone.
In a 747, however, there's no way to quickly tell whether it's a real problem, or just cellphone interference from the hundreds of great unwashed outback. Hence no phones.
This is the only logical argument I, as a layman, have encountered on this issue. The only way round, apparently, is to upgrade all civil aircrafts systems to military standards. Obviously very expensive.
Personally, I quite like having one place in my life I can escape my phone! Email, however, is another matter...