Applying some simple math here:
If an attraction has an hourly ride capacity of 1000 people per hour and Fastpass distributes 200 tickets per hour block, then 800 people in the standby line and 200 people in the Fastpass line should be able to get through in 1 hour.
If there are 3000 people in the standby line without Fastpass it would take them 3 hours to get through. With Fastpass, it would take them 3 hours and 45 minutes to go through. Increasing the wait time by 45 minutes. However, what everyone seems to willfully ignore is that in that 3 hours and 45 minutes an additional 750 people with Fastpass will also be going through the line for a total of 3750 people.
Your hourly ride capacity doesn't change. The standby line is increased, but the only people that are at a disadvantage are those that choose not to get a Fastpass.
This math applies to all attractions. I don't really understand the argument that it works for some attractions and not others. Math is math. Unless there is something in the Fastpass system that lowers the hourly ride capacity for attractions, the system is sound.
The people in the standby line are choosing, not to wait in a single que of people, but in a single que and a virtual que as well. Fastpass patrons are only waiting in the virtual que.
Your math is correct and faulty at the same time. FP isn't just allowing people on the line...it's shifting guests to a later time. I'll give a simplistic explanation, because FPs are issued all throughout the day and for varius times, but we'll stick to even hours for the example.
Attraction has a capacity of 1000 guests per hour, and issues 350 FPs.
Let's say at 10:00am there are a 1000 guests queued up, making the wait an hour. However, 350 FPs are available at the FP distribution machines starting at 10:00am. Those 350 FPs are NOT for the hour of 10:00am to 11:00am. They will be relegated to the next hour based on when, during the hour of 10:00am, a guest has grabbed it. It's more like a reservation system at a restaurant...the difference being that only a few spots are reservable. FP is shifting riders to a later time. If the people who grabbed a FP didn't have that option, they would have gotten into the standby line, bringing the numer of guests queuing to 1350 and driving up the wait time to 1 hour and 17 minutes.
So now we arrive at 11:00am - 12:00pm. FP returns drive up the standby wait time to 1 hour and 17 minutes. Had the FP guests not gotten the FPs and got in line during the 10:00am - 11:00am window, then the wait time for that hour (10am-11am) would have been 1 hour and 17 minutes instead of only 1 hour. So without FP the standby wait times would have remained unchanged.
This of course assumes constant attendance with no fluctuation, but it is only an example.
This system, of course makes the assumption that people who grab a FP would have gotten in line anyway, so the wait time should be the same. Guests who don't return period and guests who show up later cancel each other out. There might be an increase in wait times for non-FP attractions or even another FP attraction because now a guest is in two places at once, however I think the effect is minimal.
Disney is making the assumption that without FP, those guests would have most likely have gotten in line anyway, so a guest in the standby line isn't waiting any longer. Ideally the guest is in line for food or shopping. And keep in mind that the FP holder actually waits longer than the standby. The only difference is they aren't actually in line.