The struggle continues
This is a disappointment, but it needs to be kept in perspective. The IWW was formed in 1905, decades before the National Labor Relations Act was signed into law by Franklin D. Roosevelt. There was no legal process in place to recognize unions at that time: for the first few decades of its existence, the IWW didn't sign any contracts at all. Agreements between management and unions were completely informal. They were enforced by the power of the union to go on strike or find other means of disrupting the company's operations if the company offered substandard wages and working conditions. It was a rough and intensive process, but it worked: using a variety of direct methods, the union was able to bring about improved conditions in the industries where it had a significant presence.
Government doesn't create unions. It only recognizes them and allows them a limited number of powers under the law, none of which mean much if the union doesn't have the power to enforce them. Under the NLRA, the employer is required to bargain in good faith with a union that has won certification, but they are not required to sign a contract with that union. Many unions have found this out the hard way after winning NLRB certification and finding that the employer refuses to deal.
If you read the National Labor Relations Act itself, available online, it says right in the beginning that it was intended "to eliminate the causes of certain substantial obstructions to the free flow of commerce and to mitigate and eliminate these obstructions when they have occurred". In other words, it was written to allow business as usual. The entire first section of the Act is an attempt to argue that legal unions and collective bargaining are good for business.
Needless to say, business has never really believed this, and unions shouldn't either. Collective bargaining is only good for business in the sense that strikes and other forms of direct action are much, much worse for it. Workers forget that at their peril.
The best side of the Act is that it does protect concerted activities on the part of workers, whether or not they are represented by a union. No doubt the JJWU will make good use of that power as they continue their struggle. Many people will be watching Jimmy John's to make sure they respect it.