...Did I purchase a money pit? Why does it seem there are an extraordinary number of problems and issues with these vehicles? Are people just unlucky? Are they abusing their vehicles? I have had mine for 2 weeks--'06 3.7 It had 42,400 miles on it when I bought it. Only thing so far is the left front directional is not working.... I'm getting real nervous about these problems people say they are having. I guess only time will tell...
I've had my Q1 V6 '08 Commander for almost a year (purchase date was in late August '08).
It's had one recall - the key fobs. Seems that the release spring on the '08 fob was weak and the fob came off of the valet key too easily. Fixed under warranty.
No other issues. None. Nada. Zip.
I wouldn't get too worked up with what others are keying into an Internet forum.
Some of the reasons you seem to see a lot of questions and complaints on the forum are that (a) many members modify their rigs and have questions, or break something while doing a modification (b) if something does go wrong it's posted here as an FYI and may garner many responses and (c) people love to complain. Another is - who bothers to post when the thing is running great??? Unless one reaches a milestone like 300,000 miles or some such, there's no news in "everything is fine".
Not to say the early Commanders didn't have issues. I learned long ago not to purchase version 1.0 of anything unless I was prepared to be a beta tester. (I had a lamentable experience with one of the first Chevy Vegas off of the line. Taught me a valuable - albeit expensive - lesson). However most of the issues on your '06 will have been sorted out by now, I should think.
I like my Commander, feel comfortable in taking it anywhere (this week my wife and sister-in-law drove mine from Detroit to Pittsburgh and back; if it weren't a trustworthy vehicle I would've suggested a different ride), I perform as much of my own maintenance on the Jeep as I can and go by the book on fluids and service checks.
If you look at some of the complaints they are about the amount charged by dealers for relatively simple service procedures. The problem there isn't the Jeep, it's the Jeep dealer. (Not that they don't have to make a living too; I'm just not willing to spend that kind of money on a procedure I can do myself on the driveway on a sunny afternoon).
Also - a lot of folks on the forum really do take these things off road; more than I would have anticipated. That creates the need for more frequent maintenance procedures, fluid changes, tire issues, etc. But at that point you're just not paying for the Jeep, you're paying for your hobby, too.
The bottom line - I doubt if you've purchased a money pit, unless you've had the misfortune to buy a Commander that has been abused by previous owners.
Relax and enjoy your Commander. Mine doesn't go off road (intentionally, anyway

) but it gets through the winter weather quite well and is an enjoyable ride in the summer.