There's multiple kinds of liquor licenses.
You can be a bar or restaurant that serves alcohol (retail consumption license).
You can also be a brewpub (restricted brewery license), which comes with production limits and requires the above.
You can be a brewery, which mostly makes and sells beer to retailers and distributors to consume elsewhere, but might have some tasting events (limited brewery license).
New Jersey strictly limits the number of liquor licenses of different types. Limited brewery licenses don't count against these limits: it's expected they're mostly selling their goods to other licensees.
It might be protectionism, but more likely it's just an effort to regulate alcohol that doesn't take into account the changes in the craft beer scene in the last couple of decades.