What is correct to say about the satire in Jonson's play is that he is satirizing fools, crooks, and swindlers. Biographers have not succeeded in definitively identifying Jonson's personal opinion about alchemy, itself, though he obviously scorned the use of alchemy in crooked practices and swindles.
The way we know that Jonson is satirizing crooks and swindlers and not practitioners of alchemy is that the characters are obviously identified by their character names. This style of naming makes this play an allegory, which makes Jonson's point obvious and clear. Some of the allegorical names follow. Lovewitt is trusting but of low wit (low intelligence) as he leaves his home without hesitation in the hands of untrustworthy and unscrupulous fellows. Subtle is the one who is the Alchemist.
When all your alchemy, and your algebra,
Your conjuring, ...
Could not relieve your corps [body] ....
His allegorical name implies his art and skillful manipulation of the swindle and of the fools being swindled. Face is the nickname of the intermediary who finds the fools and introduces them to Subtle. He has been helped by the Alchemist's skills:
[Have I not] Giv'n thee thy oaths, ...
Thy rules to cheat at horse-race, ...
Made thee a second in mine own great art?
His allegorical name implies his ability to be changeable and effectively convince fools to enter the swindle. These allegorical names, which identify character types, prove the satire is aimed at fools, crooks and swindlers. If Jonson had chosen characters earnestly pursuing alchemical experiments in material composition who affected people's lives for the worse, it would be easy to assert that the satire was aimed at practitioners of alchemy. Since this is not the case, an analysis of the play as satirizing alchemists is more difficult to make. Though it may be said he sees them as one of the fools.
Alchemy was the pseudo-science--in an era when science was young and untried--of creating molecular change in material objects, especially metals. The belief was that metals could eventually be forced to transmute (i.e., change) to gold. Scientific practitioners believed that proving this transmutation would open the doors to understanding the properties of the material world, much like today's particle physicists believe experiments at CERN's Large Hadron Collider will open the doors to our understanding of the quantum world. Of course, less scrupulous practitioners sought to master the secrets of alchemy for the wealth of the gold itself, but these sorts were not the only practitioners.
This discussion of the goal of alchemy reveals its metaphor. Alchemy is the metaphor for chasing ultimate knowledge; it is the metaphor for attaining ultimate wealth; it is the metaphor for ultimate understanding of life's mysteries. In Jonson's play, alchemy is the metaphor for ambition chasing ultimate greed and wealth. Yet, there is a second metaphor that may be recognizable. In his comments in "To the Reader," Jonson compares the comedies of his contemporary playwrights to swindles by asserting that they are full of foolery and vastly far from showing human nature. Thus the second metaphor represents his peers' plays:
thou wert never more fair in the way to be cozened, than in this age, in poetry, especially in plays: wherein, now the concupiscence of dances and of antics so reigneth, as to run away from nature, ... ("To the Reader," Ben Jonson)