One of the theories about this was related to water resistance. Many people use their phones while waking. If the headphone jack is on the top and not in use, it's a gaping hole that could let in raindrops. I remember Apple Geniuses were trained to look for the moisture sensor in the headphone jacks on the older iPhones as part of any troubleshooting.

On the bottom, it's somewhat shielded. I was looking up waterproof 3.5mm jacks earlier, and the raw parts for this were about 9-10mm in height when mounted to a PCB. The iPod touch is at 6.1mm and the iPhone 6 at 7mm, not really leaving room for one of these waterproof designs for the jack.

The iPhone 6 and 6s show hints that Apple is working to improve the water resistance of the product. Improvements between the 6 and 6s in particular were examined by iFixit on a second teardown.