When I download a zip file through Safari it automatically extracts it into a new folder named as the ZIP file is. Is there a way to disable the auto extract feature and just leave the file as is in ZIP format?
In Safari go to Preferences -> General and uncheck
Open "safe" files after downloading. This disables automatic extracting of archives, including zip files. As noted below the check box this will disable automatic opening of PDFs, text documents, movies and pictures.
You can also hold the ALT (OPTION) key when clicking the download link (tested and working on Safari v6.0.5)