I'm not an 'agency', and that's the difference.
With an agency, your website's cost is based on the salaries of all of the employees of that agency and some of them may not even be involved in your project!
I will design and develop a quality site, with fast turnaround times, increased attention to detail, and more personal and responsive customer service.
Though rarely needed, I do maintain a set of freelance contractors that I use whenever a project will benefit from a specific set of skills.