Yep! Go to "accounts" under Sys. Prefs. And click on "Login Items" from the row of options in the "accounts" window. You should see a list of applications in the box. To the left of each item, there is a box to toggle whether that program is hidden at startup. To add/delete an item to the list, click the +/- buttons below the items box.
Hope thats clear!
And I also hope you meant "hidden" as opposed to "minimized". The easy way around this is that if the program is hidden, and you want to see its window, just click on its icon in the dock, and the app's window should pop up, just like the Finder does.