In the case of web development, there is plenty of natural integration that you get in the browser that is simply not possible with a native tool...for instance the simple ability to integrate with other web components with little effort, in the case of our product we provide a WYSIWYG editor via the tinymce component, that took little effort because it was a web component integration. A browser IDE can integrate with in-browser developer tools such as those on Firefox and chrome.

Then there are the advantages of hassle-free remote access to application assets...this may not be a big deal to a dev who likes git, ssh..etc, but for many developers being able to access and work on their apps simply by loging into another web app is preferred.

Browser IDE products themselves are inherently easier to develop, I know I am happy to be building a web app instead of Java swing components, years ago I attempted to build a native IDE (http://bit.ly/IwZCEL), I am glad I am not doing that today:)

These are just some pluses, there are all sorts of ways that the browser,web and web-application development just fit together.