I have seen a lot of people shying away from Linux because they think it is not as user friendly as windows. However, the ground reality is that more and more people are choosing the Linux virtual server model for their web hosting needs. The main reasons for this are the flexibility and rock solid security that you can get from Linux kernel. In the long run it also turns out to be more cost effective than other VPS solutions.
If you are planning to start an e commerce business and want to stay in the business for long then you will require a stable server for managing and running your site. I can tell you from my experience that you cannot go wrong with a Linux dedicated server. Linux is no longer the geek friendly OS devoid of a nice GUI! A lot of people choose the Apache server. What you get from this platform is flexibility and enhanced security.