All software that is run by vcenotes.com is either open source or internally developed (by volunteers). So yes, this site was created for 'free'.
The main costs incurred by the ongoing running of the site however, are much more significant. Firstly, as GerrySly pointed out, a domain name needs to be registered and maintained (around $20/yr or so). More significantly, however, is the cost to host this website on a resilient load-balanced server setup and the associated bandwidth costs. Given the amount of traffic we see, especially around this time of year, this can be quite significant (this cost is mostly offset by advertising revenue, however).
tl;dr - running a site this size is not cheap, setting it up might be. A small sized site can be run on a shoestring if needed due to the quality of open source software available and the existence of free (or cheap) non-mission critical hosting services that operate
