Blender stores a lot more mesh information than an STL file.
An STL file is a basic «geometry only» file format suitable for 3D printing and fabrication processes, it saves little else beyond the geometry itself. There is no color, UV coordinates, normals or anything else saved in the file.
A blender file has much more complex geometry system suited for a lot more than just fabrication processes.
It stores not only geometry, but also UV Coordinates, vertex colors, normal information, mesh selection state, vertex groups, among others, it also stores the geometry itself in a much more versatile format allowing complex geometries beyond triangles, like quad faces and NGons.
Besides that there may be other complexities involved like inefficiencies of the file format/application, file compression, or data caching.
Under the menu File > User Preferences > File > Save & Load you will find a Compress File option, which if ticked should have Blender store information in a much more compact way.