You can tell Padrino what you want during the creation of a new project.
You can tell Rails what you want immediately after the creation of a new project. Rails simply saves you time by having sane defaults. Convention over configuration at its best.
Padrinos fundamental philosophy is to be a framework built up of independent components and with limited opinions. Rails is by default opinionated: You can swap out certain components but all in all you're expected to do stuff "The Rails Way". That's the difference. It may or may not matter to you and in many ways produce the same end results, but the approach still differs.
