I think you're extremely overselling the complexity of things. Sure, there's a lot of layers and parts involved in making web pages work and in the popular web development ecosystem in general, but they were usually created to solve specific problems, and knowing of them can help you recognize how problems you may run into may be solved. None of them work by magic or are beyond comprehension.
The browser speaks the HTTP protocol to a webserver, and receives primarily HTML. The HTML is styled with CSS and can execute Javascript. Javascript running in a web page uses the DOM (Document Object Model) to interact with the page's HTML.
Javascript bundlers (Browserify, Webpack, etc) let you modularize your code across multiple files and bundle it up into a single output file for browsers to download. Javascript minifiers exist to strip out everything from a Javascript source file that's not strictly necessary to execute it (comments, whitespace, original variable names, etc) in order to make it smaller for download. Various compile-to-javascript systems exist: Babel to let you use upcoming Javascript features, Flow and Typescript to let you use annotations for static typing, emscripten to let you C/C++ on the web, etc.
Like any other popular programming language, there's a healthy ecosystem of libraries for Javascript. There are a lot for algorithms and data structures like any other language, and you also have plenty specifically for adding abstractions to using the DOM. The DOM is definitely usable on its own, but many applications benefit from using abstractions from libraries to interact with the DOM. This isn't very different from the popularity of GUI libraries (Qt, GTK, MFC, wxWidgets, etc) in desktop applications over the raw OS windowing APIs. jQuery provides a fluent API for manipulating sets of elements directly. React provides a system for making modular user interfaces taking some inspiration from functional programming and de-emphasizes manipulating elements.
All of the parts mentioned above were introduced to solve a specific problem. If you understand the problem they were built to solve, then their designs are often intuitive. If you don't currently understand the problem they were built to solve, then (for anything after the 2nd paragraph) you probably haven't hit that problem and often don't need to use them.