A decision to not prosecute does not necessarily mean that a crime was not occurring. It may mean that the evidence is not strong enough to get a conviction worthy of the resources spent on it or that the potential downside of continuing the prosecution (as of a journalist) outweighs the punitive measure against the accused.
It's a fair point -- but in the Wentz-Graff case, the police never stated to her or anyone else what crime she was suspected of. The police seem to be running with "oops, we didn't know she was a journalist", which seems implausible given the clearly visible press card in the photographs of her arrest.
Of course, any one case can be put down to incompetence, but this isn't just one case. The SJS editorial linked from the TFA gives other examples, as well as a fairly measured commentary which takes into account the difficulties faced by police.
I agree with you that the explosion of "citizen journalists" creates a bit of a grey area here, but most of the cases under discussion seem to involve salaried, credentialled, professional journalists and reporters taking pains to advertise their status.
Maybe it is just incompetence all round, but the effect is the same whether or not this is a planned policy: journalists are discouraged from reporting on protests by fear that they will be arrested.