The filesystems on the device that are accessible via USB are actually MS FAT types, whereas the device runs Linux as the OS. Unix file permissions are really a kludge when applied to FAT filesystems, so I'm not surprized that you can't really change them exactly, especially when going through the USB Mass Storage interface. However, rwxr-xr-x should be fine for running qorganizer.
Looking at my previous suggestion to run "./qorganizer" in the applications directory, I see now what might have been your problem. qorganizer looks to be the name of the directory, and qorganizer.app the name of the executable file. So, you probably would get a permission denied error if you tried to "run" the directory using that command. Did you try to run "./qorganizer.app" from the applications directory rather than "./qorganizer" when you saw the permissions denied error message?