When working on proposals for new work, I often get a raised eyebrow when someone hears that a simple app can cost a lot more than a large website. They think because the app might only consist of a single page and the site hundreds that the site is somehow much harder to put together.
When pondering this, I came up with an analogy… condos vs cottages. A condo can house many families while a cottage is generally for a single small family. If this is true, then why is it sometimes it can cost more to have a cottage built vs having a string of condo's built. The answer is simple… customization my friend, customization.
An online/web app may be smaller in size than a large website but believe me it usually takes a lot longer to build one out, and I can almost all but guarantee that the final product will have much more custom work in it than your standard website.
Note, that this is not ALWAYS the case, but in my line of work more times than not this rings true.