There is some difference between the hardware that Cisco uses for its
routers v.s. what most Linux vendors offer, which is the Intel x86
platform.  Whether or not these differences really amount to anything is
another religious argument.  Without knowing the intimate details
involved, I cannot give advice either way.  Instead, I'm going to give
you a link to a Linux vendor that thinks they have the answer:

http://www.vyatta.com/download/whitepapers/Vyatta_Better_than_Cisco.pdf

Now, determining whether or not their claims are based on fact or simply
marketing is an exercise I leave for you.  I do know that there is
plenty of quality x86 hardware out there, and Linux knows how to do even
the trickiest of routing and firewalling.

Sorry if that wasn't really an answer you were looking for.  It's late. ;-)

Chad