Adam Smith supported them and he was no mercantilist. Here is another take:
…that remains the consensus view among a broad sample of modern scholars: a recent study concluded that nearly 90 percent of the economists and historians surveyed agreed with proposition that “[t]he costs imposed on the colonists by the trade restrictions of the Navigation Acts were small.”
if the burden of the Navigation Acts was so slight — no more than one percent of GDP, according to Thomas’ calculation — why did the Americans make such a fuss over it? The short answer is that although the burden to the American colonies as a whole was low, it did not fall evenly across the entire economy: some sectors and regions suffered disproportionately, while others were barely affected. The regions and sectors that suffered the most from the Navigation Acts tended to be the strongest supporters of the American Revolution.
That is from the forthcoming useful book by Richard S. Grossman Wrong: Nine Economic Policy Disasters and What We Can Learn from Them. For the two relevant Robert Paul Thomas pieces (jstor) see here and here.
To further brighten your day, here is a non-gated piece by Robert Whaples, “Where is There Consensus Among American Economic Historians? The Results of a Survey on Forty Propositions” (pdf).