The decision was made that being acquired by Redmond would not be in Yahoo's “best interests”, and believes that Microsoft offered way too little for the company. They assert that even if the company is having hard times, $44.6 Billion is simple too little of an offer and undervalues what Yahoo is worth. They probably have a good point – everything else aside, Yahoo holds a larger share of the search market than MS does. And that's exactly what Redmond is after.
That's not to say that discussions are over. Often initial bids are rejected, with the buyer then coming back with something larger. That's probably what we'll see here, with MS coming back with a larger offer in the near future.