Ahh. I see. To me, that's just "stuff you run on the phone". The ecosystem is the whole intertwining of Apple products: you don't get a media server, you get an AirPlay. You don't just have a wifi router, you have an AirPort. You don't just drag files to your iPod, you need iTunes on your computer to sync them. You don't just use a micro-USB charger like the rest of the world, you need an Apple Lightning connector.
Lots of that is easily avoided (a wireless router will work fine), but Apple works very hard at making a ton of disparate products integrate pretty deeply. As I said, that has it's upside: if you are an all-Apple household who goes with their way of doing things, the experience is pretty seamless. But there are times when it can get frustrating if you need or want to do some things in a different manner than they envisioned.
There was a class action suit about it which looks bogus, but problems with the home and power buttons are pretty prominent if you google:
http://tech.fortune.cnn.com/2013/05/15/apple-iphone-button-lawsuit/
Some of the struggles with the supply line's quality control have been pretty public:
http://www.theregister.co.uk/2013/04/22/apple_returns_iphones_to_foxconn/
Anecdotally the home button's been an ongoing issue since the early iPhone days, while the Lightning charger seems to have fixed what was a fairly common problem with breaking charger slots on the 30-pin chargers.
I think these are all fine points with an added note that YMMV.
I've been using iTunes since I was using iPods in junior high school. The program has gotten better and it's become the easiest and best place for me to find and discover new artists, new apps, and see what books are available.
Where you see a problem with not being able to put music on the phone without iTunes (there are alternatives), I see a program that organizes my music for me and is a one stop shop. I don't have the patience for the manual process anymore. I download a song and it's on every device immediately. If I download a non-iTunes song, it's on every device immediately (iTunes Match). Same with apps, books, calendars, pictures....
The combination of iCloud and iTunes Match for me is incredibly powerful.