There doesn't seem to be a tool to mass-upload all RDL files in a directory, so I created one. It's available on BitBucket here: http://bitbucket.org/emil/bulk-rdl-uploader-for-ssrs-reports/overview/
The executable is available here: http://bitbucket.org/emil/bulk-rdl-uploader-for-ssrs-reports/downloads/ReportingServicesBatchUpload.exe
This is a console application with no dependencies (it calls a web service). Call without parameters for usage information. One known bug is that the "create a folder if it doesn't already exist" logic seems to be broken for some servers, so for best results create the reporting services folder prior to running the program.