First, I think it is my due diligence to mention that without asking users in one way or another all you can rely on is speculation and generic user behavior patterns. Qualitative research is needed to answer this question better.
To answer better would require more info, such as images of the 2 navigation options, but I will offer a few possibilities here:
Less Work in Context
As you mention, if a user has read the page and is at the bottom of the screen, they will then consider what they want to do next. The convenience of having the footer in front of them will more likely lead them to interact with it.
We communicate through words and word choice is key. If the terms used in the main menu differ from the footer, it could lead to user preference.
Its possible the navigation terms in the footer provide more information scent (fancy $5 term for links or buttons closely matching what a user is looking for). If the footer uses terms that users are more familiar with, they will likely use it more.
In some cases, main menus require interaction: click or hover to display the menu, click or hover through a series of dropdowns, multi-click iterations to navigate through categories, and more. This is effort.
Compare this to a footer, which likely displays all links in a list; no need to do anything other than click on the name of the page you want. If a user can put in less effort for the same result, they will.