Paranoid about remote key

As a new owner I have been shell-shocked by the high price and technical complexity of getting a duplicate remote master or even valet key made for 2007 Accord V-6.
One online accessories/parts site sells a small leather case that protects the key and has a see-through plastic face for pushing buttons on the remote.
Is it paranoid to get something like this to "protect" the key?
And why do all keys have to be available and reprogrammed when a copy is made? Can't the existing key and its security code by cloned or does the anti-theft systen actually remember and read each key separately???
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