I think The Alchemist and the story of it main character can be read as an allegory, depending on what you define as an allegory in the first place.
if you take into consideration that allegory usually entails the "description of a moral, spiritual or political reality common to all people" then this seems to fit into the plot of The Alchemist quite nicely.
There's definitely a moral lessons being told in Ben Jonson's depiction of a man called Santiago who goes out in pursuit of his dreams, which lead him to the pyramids and a quest for the secrets of alchemy captured on an emerald tablet.
On the other hand, as you can probably tell by the "outlandish" plot line that The Alchemist involves, it can also be read as a farce or tall tale too.
So it really comes down to the eyes of the reader and how The Alchemist is perceived by the individual.
The features that make it allegorical are definitely are the symbolism, the moral lessons and the personification of popularly-held beliefs through outlandish characters.
