How can I run excel from command line / cmd script such that it doesn't prompt if I want to enable macros in the spreadsheet I am running it with?
The prompt is an Excel settings so you'll need to go into Excel and change the security settings. You can change it in Excel 2007 through the Excel Options -> Trust center -> Trust center settings -> Macro Settings.
I don't know of a way to disable this through the command line, and I don't think it makes sense that you could, sounds like a security breach to me.
Signing your macros with a digital signature may do what you want. If you've signed the macros in a spreadsheet, then a user who opens it is prompted:
"Foo.xls" contains macros by Acme Software, Inc. Macros may contain viruses. It is usually safe to disable macros, but if the macros are legitimate, you might lose some functionality.
The user will get the usual Disable / Enable Macros choice, but she will also get a bonus option:
Always trust macros from this publisher.
If the user selects that option, she will never see the prompt again for this file or any other signed by the same publisher.
Here are instructions on how to get a certificate and sign an Excel 2007 file. If you're using Excel 2003, read that and then read these instructions on signing an Excel 2003 file.