The primary reason is that you want keep two wallets. One you treat like a safe-deposit box, keeping the secret keys strongly encrypted or on removable storage

The primary reason is that you want keep two wallets. One you treat like a safe-deposit box, keeping the secret keys strongly encrypted or on removable storage and only loading them onto very trusted computers to make transactions and then wiping them. The second you treat more like the eponymous 'wallet' and use for day-to-day stuff where the constant security measures would be impractical. Thus, you occasionally need to transfer money to/from your two accounts. There is, of course, the additional measure of creating yet additional accounts to which funds are transfered for the sake of making payments that you want more anonymized (read: not traceable back to an account you use more commonly for possible more legit stuff).