The problem with a zip is that you aren't really sure what's inside of them. You would need to unzip the contents, scan for virusses and then you know that there aren't any known virusses in them.
Second of all, when fileuploads are in use, you can only allow a certain amount of file extensions (white list rather than blacklist) and you need to verify that the files with this extension are indeed of that type (for instance a .bin changed to .txt). But every type of file can be encapsulated in a zip file. If you whitelist .zip and you don't check the contents, you are actually making the whitelist obsolete. So again you would need to check the contents of the zip file to make sure only a certain type of files are included in them.
So zip would only be feasible in the event that you need to reduce large file uploads that might congest the network. Because to provide security you would still need to unzip them and check the contents. If you are doing this because you are thinking about conserving diskspace, you are better off accepting the files in normal format and then zipping them yourself after you have checked them.