What is the difference between rubber top and metal top corny kegs?

Generally speaking, the question is the answer. The difference is that rubber top kegs have rubber tops where as metal top kegs are missing the rubber. Going beyond that, there are a few other differences which may, or may not, matter for you.

Beside the obvious difference between rubber top and metal top corny kegs, there are a couple other benefits (in our opinion) to rubber top corny kegs. The rubber tops on corny kegs serve a couple different purposes:

Rubber top kegs are much easier on the hands when you're carying a full keg around. An empty 5-gallon corny keg weights about 10-11 lbs. A full 5-gallon corny keg will weigh about 50-53 lbs. Having a dual rubber handle makes a full keg much easier to handle when you have to move it. Metal top kegs are simply a single metal strap and lugging a full 5-gallon keg around by a metal handle can be a bit tough and uncomfortable.
Rubber top kegs help to protect the keg lid and posts. Let's face it, kegs get knocked around and even knocked over from time to time. When a metal top keg gets knocked over, the post(s) can be subject to damage if they hit anything, whereas a rubber top keg greatly helps to protect the keg lid and keg posts. Take a look at the picture below, this keg was damaged during shipping (not an uncommon thing), but this same type of damage can occur through normal use.

In our opinion, the cost savings of a metal top keg vs a rubber top keg, about $10-15 in most cases, is not worth the risk of having damage to the working components on the top of the keg. Think of the rubber top on kegs as a bit of an insurance policy against damage to the necessary/working components on the keg. In addition to the added protection you get with the rubber top, you do get a keg that is much easier to handle when full.

If we were to point out a con or a negative aspect of rubber top kegs, it could be that when rubber top kegs get very old and mistreated (i.e. left outside in the sun and elements for years), the rubber loses its seal and when it gets wet, it can leave black marks (or red/blue/green if you're dealing with old pin lock kegs with red, blue or green rubber)