Personally, I find it easier and quicker to do it via keyboard. Especially when there are a large number of files. For example, how would I do cp *.com another-dir/ in a GUI? Imagine if the folder has abut 300 files with different extensions... Yes, cp, mv, rm are safer. And easier.
While I'm not disagreeing with you (I, too, am a *nix greybeard who loves the command line), it's definitely possible.
In Nautilus, do click 'Edit | Select Pattern' (or hit Ctrl+S). Type *.com in the text box, click 'Ok' and then ctrl+drag the files to the 'another-dir' folder.
The thing I find Nautilus lacking is in certain recursive operations. For instance, it isn't possible using Nautilus to automatically change all permissions in all directories recursively under 'foo' to 'rwxrwxr-x' without doing a 'Select All' at each directory level, right clicking, and then clicking the right check boxes. You have to do this for EACH directory level. At a bash prompt, I can just do 'chmod -R 775 foo' and be done with it.
