1. As said by other posters, CrossFit is huge. And it's not like McDonald's - there's a large amount of variation that's inherent in an organization that barely looks at its members. Instructors are free to come up with whatever program they want.
2. Most personal trainers know absolutely nothing about actually training people. They know what works for them, but they have a very hard time in applying workouts to other people. The workout plan that fits a 220-pound male rugby player is not going to fit a 110-pound female volleyball player or a 350-pound couch potato who is trying to get into shape. Applying the same program to these three people is going to lead to disaster.
3. Crossfit is different from traditional weightlifting, which seems to attract a certain class of people. These people basically say, "I made this switch, and it's done wonders for me! The old paradigm is flawed, and you're an idiot for sticking with it!" You'll notice this incredibly annoying group of people whenever there's an alternative - religion, programming languages / frameworks, etc.
4. Apply #1, #2, and #3, - a very large organization with idiots who loosely fall under it, and a group of people who look down on anyone who isn't a member, and you get a group of people who are really, really easy to hate. And, to some extent, it's completely true. You get the stereotype of the typical CrossFit user who won't shut the fuck up, makes fun of people who go to "regular" gyms, and doesn't actually know what he's talking about. It leads to the jokes of "The first rule of CrossFit is to talk about CrossFit" and "A CrossFit workout isn't complete until you post it on Facebook."
My own experience with CrossFit is that some parts are perfectly fine; there's absolutely nothing wrong with circuit courses, and there's nothing wrong with explosive movement. The problem is when you start doing exercises that require lots of weight and proper form and then CrossFit them - doing as many reps as possible as quickly as you can. Push-ups? Go for it. Burpees? Be careful, but go for it. Snatch, deadlifts, and pull-ups[1]? No, and run far far away before you tear your rotator cuff.
The last thing is that CrossFit doesn't seem to have a goal in mind. As Mark Rippetoe states, "Exercise is physical activity for its own sake, a workout done for the effect it produces today, during the workout or right after you're through. Training is physical activity done with a longer-term goal in mind, the constituent workouts of which are specifically designed to produce that goal."[2]
This is supremely important. Even someone whose goal is as simple as "Lose weight" and "Look more muscular" needs a training goal, not an exercise goal. CrossFit doesn't seem to deliver that. They talk about their goal being all-around fitness, but they don't have a good methodology for doing so. Take a look at what decathletes, strongmen, and even the CrossFit Games athletes are doing - it certainly isn't CrossFit. That, in and of itself, should let you know that something is badly wrong.
[1]http://cdn.styleforum.net/3/37/314x314px-LL-375a6e39_TooBO.g...
[2]http://www.t-nation.com/training/crossfit-the-good-bad-and-t...