if popularity is the main reason, then how come the more popular unix servers, are more secure than their windows-based counterparts?
why unix better? by obscurity? absolutely not (i reiterate unix are more popular, powering huge sites) better knowledge/use strong passwords? nope don't think so better admin? maybe better product? absolutely ... ssh, encription, randomization (swap, memory, etc)
my conclusion: unix is more secure due to its bottom-up iterate-often development model yielding better product (more secure, more powerful, etc)