It is easy to see how a modern day reader of this prose pamphlet of Milton's, who wrote this in the 17th century, could view it as being mysterious and difficult to understand. After all, Milton uses a number of classical and Biblical allusions as part of his argument and also uses a number of complex sentences in order to build up his discussion of free will and support his ideas. Note, for example, the following description of Truth, which is personified as a female in this quote:
Give her but room, and do not bind her when she sleeps, for then she speaks not true, as the old Proteus did, who spake oracles only when he was caught and bound, but then rather she turns herself into all shapes except her own, and perhaps tunes her voice according to the time, as Micaiah did before Ahab, until she be adjured into her own likeness.
This quote, which is of course a complex sentence, contains two principle allusions: the reference to Proteus who was the old man of the sea who tried to escape capture by changing shapes; and the story of Micaiah, who tried to disguise an unpleasant prophecy from King Ahab.
Given such characteristics, it is no surprise that this text can be viewed as being somewhat impenetrable by the modern day reader. However, interestingly, it is also important to appreciate that this text is actually an incredibly sophisticated example of rhetoric, for all of the challenges that we may have today in understanding it and engaging with it. Its structure clearly bares the characteristics of classical rhetoric, and its original subtitle was "A Speech," which helps explain the florid, oratorical tone of the tract. In short, although it is difficult to understand for many reasons, it also has many merits that make it worthy of further study.