I have to create secure, password protected .pdfs for my clients many times in one day and grow tired of having to type in the password twice each time I save a .pdf.
Is there any way to automate the password part so it puts it in without me having to type it twice everytime?
Not in InDesign. It might be possible with the Action Wizard in Acrobat Pro but I'm not sure. Ask in the Acrobat forums.
why dont you use cirtificate instead?
Grant's point is a good one, but setting up a certificate would need to be set up in Acrobat Pro.