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They want to be the sole infuser of ads into Twitter streams.

Twitter has a right to protect the quality of their stream.

With 140 characters, there's no room signature spam.

Twitter's policy that you can't alter the user's tweeters is one of the first thing a developer sees in the terms of use.

The problem, I believe, is that they don't want users to be confused about where ads are coming from. Ads embedded in update streams may seem to be coming from twitter. Many other twitter clients have ads, they just make sure they can't be mistaken for ads embedded in updates.