Is a Linux desktop more secure? Well yes and no. It depends on which desktop you chose, how you configure it and what you do with it. In the past, Windows desktops often came installed, by default, with some very poor security controls. For example, there was no default firewall and no requirement to use a password. Some of these deficiencies have been corrected in XP and it is my understanding that these controls will be further enhanced in Vista.
In comparison, it is my opinion that most Linux desktops tend to be more secure due to things like firewalls and password installation by default, in terms of their base configuration. But in both cases you can configure, harden and lock down Windows and Linux-based desktops to ensure a higher level of security than they come with. As a result, it is very hard to say which is the more appropriate option, especially if you ignore the other factors in selecting a desktop -- cost, user skills, manageability and functionality.
My recommendations is to configure the appropriate desktop for your environment that provides a secure setting at an appropriate cost and won't compromise your user's ability to perform their required functions.
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