What it's "intentions" were when it was passed is irrelevant to what it's effects were in operation. Year after year we see these bozos up in Washington declaring they are passing some such thing for some such purpose, and invariably it ends up doing something else and which is much worse than we were led to believe.
Remember the "Patriot act"? How's that looking now?
Let's say I believe their intentions were good, but invariably any law is twisted by immoral players into something they can use as a tool or a weapon. The Navigation Act was no different.
There were successful Southern shipping companies with the Navigation act in place. Had it not been for that law, the Southern shippers would have lost out entirely to the British shippers.