Using Linux as a router gives you a lot of possibilites and control. Also the software is free, software is customizable, and the hardware can be upgraded when you need more functions.
The possibilities of a Cisco router depends on the model that you selected.
Your question is "why am I using a Cisco router instead of setting up Linux to be used as router?" When someone ask you what router you are using. You can say its a Cisco router blah, blah, blah. For some people when they state a quality product to their friends and callege, they feel warm and fuzzy inside stating their product. Then all hail breaks loose when bragging and ego kicks in.
You can use either one. They are both great. However depending on your expertise with Linux, it may take a while to setup the firewall to have a almost secure network from the internet.
Use nessus to check the security of either devices after you think you got them setup properly.