Are you sure you've quoted him correctly? Let's look at the actual letter to James Madison to find out:
I presume that, having spared to the pride of England her formal acknowledgment of the atrocity of impressment in an article of the treaty, she will concur in a convention for relinquishing it. Without this, she must understand that the present is but a truce, determinable on the first act of impressment of an American citizen, committed by any officer of hers. Would it not be better that this convention should be a separate act, unconnected with any treaty of commerce, and made an indispensable preliminary to all other treaty? If blended with a treaty of commerce she will make it the price of injurious concessions. Indeed, we are infinitely better without such treaties with any nation. We cannot too distinctly detach ourselves from the European system, which is essentially belligerent, nor too sedulously cultivate an American system, essentially pacific. But if we go into commercial treaties at all, they should be with all, at the same time, with whom we have important commercial relations. France, Spain, Portugal, Holland, Denmark, Sweden, Russia, all should proceed pari passu. Our ministers marching in phalanx on the same line, and intercommunicating freely, each will be supported by the weight of the whole mass, and the facility with which the other nations will agree to equal terms of intercourse, will discountenance the selfish higglings of England, or justify our rejection of them. Perhaps, with all of them, it would be best to have but the single article gentis amicissimæ, leaving everything else to the usages and courtesies of civilized nations. But all these things will occur to yourself, with their counter-consideration."
Let's look at some unadulterated quotes from Jefferson on commerce:
Our interest [is] to throw open the doors of commerce and to knock off all its shackles, giving perfect freedom to all persons for the vent of whatever they may choose to bring into our ports, and asking the same in theirs.
The exercise of a free trade with all parts of the world [is] possessed by [a people] as of natural right, and [only through a] law of their own [can it be] taken away or abridged.
An exchange of surpluses and wants between neighbor nations is both a right and a duty under the moral law.
Nature . . . has conveniently assorted our wants and our superfluities, to each other. Each nation has exactly to spare, the articles which the other wants. . . . The governments have nothing to do, but not to hinder their merchants from making the exchange.
I think all the world would gain by setting commerce at perfect liberty.
It [is] for our interest, as for that also of all the world, that every port of France, and of every other country, should be free.
I am for free commerce with all nations, political connection with none, and little or no diplomatic establishment.