Assuming the charges are limited to the Daniels payment, you're correct. It's a weak case. They have to prove the misdemeanor accounting charge, then to elevate to a felony, the DA must prove that crime was used to cover-up some other more serious crime (likely campaign finance related).
The last time a similar case was brought, it was against John Edwards (who took money to pay for housing for his mistress, or something like that). He was acquitted.
But, it appears the indictment has 34(?) charges. If they're counting each check to Cohen as a charge, that's 11(?), so there's something else there. Some of that could be conspiracy charges, but we don't know.
Say my firm's database gets ransomewared. If I pay the ransom directly, that may be a particular way of accounting. But say, I pay McCohen Computer Associates to fix the problem. Why do I not book it as a computer expense? I am not an accountant but am curious how this works.
The two-step payment through Cohen is only illegal if it's done to cover up other illegal activities or it's in violation of some other law.
In this case, it's likely the hush money was funneled through Cohen to keep it off the campaign books - that's what makes it illegal.