Totally depends on what the use case is. The biggest problem is that you basically always have to compress and uncompress the file when transferring it. It makes for a good storage format, but a bad format for passing around in ways that need to be constantly read and written.

Plus often we're talking plain text files being zipped and those plain text formats need to be parsed as well. I've written code for systems where we had to do annoying migrations because the serialized format is just so inefficient that it adds up eventually.