I think there is this perception that web frameworks don't allow customization. I think people get web frameworks confused with CMSs. Most of the time frameworks are there to provide well thought-out, useful tools that are common across large applications, generally within the MVC paradigm.
Yes, you could write all of your own RESTful routing sytems, database abstraction, controller handling, package management, migration/schema tracking system, etc. But why would you reinvent the wheel, especially when Laravel, jQuery, CakePHP, Symfony, Express.js, Mongoose, etc. are going to do it way better than you are ever going to do it?
Pointing out that you could potentially have slightly more control with writing your own tools for a web application is similar to pointing out that if you wrote your application in assembly language instead of some high level language, you'd have much more power. It's silly. If you're writing a medium-sized web application by yourself or with a small team, and most of the platform you need or would want exists in some framework, you shouldn't reinvent the wheel. The framework will do it better than you 9 times out of 10.