The interesting question is not "Are linux machines infected with a cloud of malware like Windows machines?" but rather, "What factors contribute to Windows malware that don't exist for Linux?". That is, on a technical level, Linux is just as vulnerable as Windows. Fred Cohen did his initial experiments on a a 4.3BSD machine in the early 80s, so we've know about the vulnerability all along.
Linux just doesn't accumulate the uncountable legions of malware that Windows does. It can't really be "market share", as even at 1% of all users, Linux desktops probably count higher than MS-DOS did in 1988, when the "Brain" virus swept through the population. So, this Sophos-employeed blogger should shy away from his name-calling, and start researching the really interesting "why" to see if it can't be applied back to Windows.