Even if they don't use them all that wisely, as long as you are cycling people into the park with FPs, and when they leave they are replaced by more people with FPs, the standby lines are going to back up like mad for anyone who is "out" of FPs.
This could be true, but there's a question you have to ask about these people: where did they come from? Each person through the gate counts in the attendance figures, no matter how long they stay, and the attendance figures aren't showing this tremendous growth.
If a change attendance isn't enough to count for all the subjective experiences of longer lines, and we have no evidence of a dropoff in ride capacity, then one of four things must happening:
A) Guests overall are riding more attractions than before,
B) Wait times are being reporportioned in ways that favor "non-commandos"
C) Ride times have increased for some rides while decreasing for others
D) It's simply a matter of perception / selective memory.
To start with D: it's Spring Break week right now. I've noticed that over the past few months, the "Epic Wait" threads have come during peak travel periods. Regardless of the other factors, this may be coming into effect for many people, and at least influencing their results.
As to C: people have mentioned HM, Pirates, and other popular attractions as having longer lines. It's possible that some less popular attractions have shorter lines. Despite all the wait-counting websites out there, it's really hard to count actual capacities and compare one day to another from a previous year.
As to B: I really think this counts for a lot. Fuzzylogic and others have hit the nail on the head here, but the math is unassailable. As to WHY they are riding more rides than they did before, I'd guess the following: many "casual" guests probably used to spend hours in standby lines, and now they don't have to - the new system is more accessible, easier to understand, and easier to use than the old FP- system. I've read many posts on this forum where casual guests were heard to comment about how they wish they could afford fastpasses, or something like that. Also, few other regional amusement parks have similar systems, so casual guests are probably much more likely to accept several-hour waits as a matter of course. They might also have been uninterested in running all over the parks commando-style to collect FP-. It's very possible that the FP+ system is more obvious and transparent than the old FP- for the casual guest.
As to A: This option also makes sense. In effect, access to the FP+ system has turned some casual park-goers into "commandos". Again, others have done the math, but here's a simple variation. Let's say some casual guests want to spend 6 hours in the park, and the standby line is 2 hours long at 3 major attractions. So, they go on 3 rides in 6 hours, and go home. Now, with their 3 FP+, they get those rides done in 3 hours, and they have 3 more hours to kill. So, they go on more rides. Are they "happier" than they were before? More importantly, are they more likely to come back more often and spend more money? Probably.
So, I think several different factors could be causing the perception of longer lines. However, I still don't see any explanation for the general complaint that "FP+ causes longer lines." That just doesn't seem to hold water.