Here's an actual example of a CoinJoin transaction (click link for blockchain.info link):



There were 3 people involved in the transaction. There are 6 outputs, 2 per person. 3 of the outputs (coloured yellow) are for the exact same amount. It's impossible to know which of these three yellow outputs belongs to which of the 3 people just from looking at this transaction. The other 3 outputs are change amounts. We can easily tie the change outputs to the inputs, which I did by using the coloured arrows.

The guy who spent 82 BTC got back a yellow 70 BTC and 12 BTC of change - indicated by the blue arrow.
The guy who spent 171 BTC got back a yellow 70 BTC and 101 BTC of change - indicated by the orange arrow.
All the other inputs came from the 3rd guy, and he got back a yellow 70 BTC and 41 BTC of change - indicated by all the red lines.

Hopefully that makes it clearer. It's the yellow outputs that have been anonymised by this transaction, not the inputs or the change outputs.