To echo Ryan B.'s point earlier, I don't think people are confused about Twitter needing to make money. On the contrary, I think it's well-known and accepted that they need to do so in order to keep their service running. However, the way they've gone about it is both a bit confusing and counter to what made them a popular service in the first place. Thinly-veiled threats directed at their developer community, turning off the ability to find friends on other networks... I'm not sure how anything they're doing besides creating an advertising network is in the interest of turning a profit.
You could argue that sticking a knife in 3rd party clients is a push toward profitability, but many are arguing it's short-sighted and unnecessary.