Your web browser speaks HTTP. However an operating system reading the contents of a mobile device involves treating it as a block device. There is no commonly-used high-level file access protocol over USB. Unless the device can emulate an FAT filesystem over a block device interface (is this even possible without huge amounts of resources?) the device's filesystem has to be formatted as FAT.
The alternative is to create your own file access protocol and force the user to install a custom application that speaks this protocol, e.g. how iTunes interfaces with the iPad/iPhone. This really, really sucks, you now have to install iTunes everywhere.