If the line is only 5-10 minutes long, the CM's aren't collecting Fastpasses and you all wait standby. Or if you're talking about the fact your make the line 5 minutes longer, then true. But 5 minutes multiplied by how many fastpass guests per hour? That does become noticeable.
And Disney is looking to keep fastpass, but reign it in a bit. Fastpass is great for management because it gets people out of lines and into stores and restaurants. While people kill time, they are more likely to spend money. By creating a pay to play app, they are hoping to reduce fastpasses, opening up walkways and shortening wait times, while also generating revenue with the cost associated. If these passes are also provided free of charge to hotel guests, which I'm sure they will be, it adds value to staying on property and brings Disney more money.