Here's my best guess as to what is happening here. First and pretty obviously, Mueller has found nothing to clearly implicate Trump with (though the question of Trump Towers in Moscow is still in play). Cohen, since he claimed he paid Ms. Daniels with his own money, has essentially admitted to making an illegal campaign contribution. Mueller and Co., is frustrated and decided to go ahead and prosecute the more simple to prove case against Cohen, and if anything implicating Trump is found in the process, that would be great from their point of view. Additionally, if Cohen knows that they are willing to prosecute him (a la DeSouza) there's a small chance that Cohen would turn on Trump and give them something real to work with.