Why not?
You think they are going to skip 5 and call it the iPhone 6 because it's the 6th iPhone?
That would make no sense from a marketing perspective. Apple is better than that. I'm pretty sure it will be the iPhone 5, and if it's not it definitely won't be iPhone 6.
They called the 4th iPhone the iPhone 4 because there was so much confusion with 3G (data generation vs phone generation) and they couldn't release an iPhone 3G, iPhone 3GS and then an iPhone 3. People assume a bigger number and longer name means the phone is newer/better, and that's logical.
Now that we're out of that 3G confusion, I'm pretty sure the number will only designate the physical design generation.