During an interview, George W. Bush's Attorney General once was asked if it would be legal for the President to give an order to crush a young boy's testicles in the case of a terrorist scare. He responded by saying it depended on why the President felt he had to do that. This idea that something that would normally be illegal being legal if the President does it is known as the unitary executive theory.
This extreme view of the executive prerogative had its origin in Wilson and some of his immediate predecessors. In the period immediately prior to Wilson and TR, the President was considered weaker than congress. Presidential power waxed and waned after them but has been in expansion mode for the last two decades.
Wilson expanded the role of government in people's lives and crushed dissent through the Alien and Sedition act. This prevented what the government viewed as un-patriotic speech and disclosure of any government secrets. Prosecution under this law could mean anything from jail to a decades long prison sentence to execution.
Wilson lobbied congress to get the United States involved in World War I and eventually got his wish. The issue for him was that the war was extremely unpopular among some segments of the population.
German American communities were infiltrated by government spies and people that spoke out against the government were jailed. In addition, other political movements like socialism were given the same treatment. Criticism of the government was no longer covered under Freedom of Speech during war times.
The alien and sedition act is still on the books to this day and has been used to prosecute Chelsea Manning and charge Edward Snowden. This act has of course been selectively applied. It seems the Obama administration for a long time was leaking "top secret" info on all the drone strikes it carried out while David Petraeus will likely get little more than a slap on the wrist for giving his mistress access to top secret military information to write a biography about him. The theme seems to be that dissent or embarrassing revelations are punished with extreme prejudice while pro-government disclosures are allowed to slide.
I can't credit Wilson with getting us to where we are now in terms of governance by executive decree, but I can certainly say he played a role and was one of the founding fathers of the unitary executive theory.