Like Shapely (1.0 release last Friday; toot, toot!), Rtree is designed to be a specialized, highly-reusable Python interface to an industrial-strength library. It doesn't do formats. It doesn't do projections. It's not a CGI program. It's a building block that does one thing well and otherwise stays out of your way. It indexes spatial data and provides query mechanisms, and that's all it does.