Yeah, I see the "I spend so much money to come here and I expect everything to be working absolutely perfectly." Sorry, stuff happens. Monorails break down. Rides break down. The First Lady comes to appear at a fundraiser and they stop all traffic for security reasons. Cars and buses get stuck in traffic. Sometimes they break down. Sometimes the bus you're on is loading three scooters and you have to wait. Nothing you can do about it.
3 hours in a monorail is kind of drastic, that kind of thing doesn't happen all the time. In fact there is some indication on this thread that it's only happened once. Maybe that's enough for some to quit riding it altogether. I've been stuck in one for a half hour before, nothing could be done. If it makes one feel better to stick to the boats, there is that option. The ferry boats are large, and you can probably walk around them.
You're absolutely right. This is one of the MANY cases where people are blowing their worry about something WAY out of proportion.
According to Wikipedia, 50 million people ride the WDW monorail every year. I have not found any references to a stoppage like this (2-3 hours or more) aside from the 2009 reference. There may have been others over the 40+ years of monorail ridership, but none in recent experience. A Disney employee was also killed in a monorail accident in 2009 - but then again, there have been bus-related deaths at WDW too.
Hypothetically, let's say a stoppage/accident occurs once every five years. At 50 million riders per year, that's 250 million riders in 5 years. As with the stoppage, let's assume that 300 people were onboard. 250 million divided by 300 equals a 1 in 833,000 chance of being "severely affected" by a monorail incident.
Here's an interesting graph of your odds of dying by various causes:
http://www.nsc.org/news_resources/injury_and_death_statistics/Documents/Injury_Facts_43.pdf
Using that chart as a guide, as compared to being stuck on a monorail, you are:
8 times more likely to be struck by lightning.
8 times more likely to be killed in a storm.
8 times more likely to be killed by a dog.
12 times more likely to be killed by wasps, hornets, or bees.
68 times more likely to be electrocuted.
217 times more likely to choke on food.
750 times more likely to drown.
So, the most dangerous place in WDW isn't the monorail, it's the pool - or the restaurant. If you don't want to die (or be horribly inconvenienced) at WDW, ride the monorail - don't eat in the restaurants or go for a swim in the pool.