WordPress websites generate a lot of files during development which don't need to be source controlled, such as the uploads and plugins directories. To combat this you would add the directories to a .gitignore file to prevent changes to these directories being mistakenly pushed to a repository.
You also have files generated which are needed for the project, such as the phpproj files and various developer configurations etc., which would be source controlled, but aren't needed for the actual website to function and therefore shouldn't be uploaded.
Remote Explorer allows users to exclude items from upload, however these decisions aren't maintained anywhere like the .gitignore file does for repositories, and need to be selected with each upload. This opens up opportunities for human error, which could cause potentially major issues on a production website.
For example, I've just made some small changes to a stylesheet, and added some plugins which were only needed locally, and the explorer wants to upload over 4000 files, including overwriting the remote wp-config.php with my local version; the former would bloat the web server with useless files, and the latter would break the website.
I think an approach similar to .gitignore should be available when using the Remote Explorer, whereby the context menu has an option to add items or entire directories to a permanent exclusion list.