S.H.I.E.L.D is a group of members involved in saving Earth. All of those characters are fictional characters from Marvel comics. Mutants from the X-Men books are also fictional characters from Marvel comics. So why aren't any mutants from the X-Men series also members of S.H.I.E.L.D?
Answer
In the comics (Earth 616, Ultimates, etc)
For the most part, the X-Men are considered a "rogue" group. They operate outside the law and generally eschew outside authority (X-Factor being the exception to this).
As such, most mutants - and especially X-Men, would have little interest in joining up with what is effectively a government controlled military group.
That said, Skids - a Morlock, and a member of X-Factor and the X-Terminators did become an Agent of S.H.I.E.L.D.
Kitty Pryde was recruited by the then-acting commander (G.W. Bridge) to become a temporary agent of S.H.I.E.L.D
More recently, Alison Blaire, a.k.a Dazzler has been recruited to S.H.I.E.L.D as a former X-Man who may help provide insight into Scott Summers' line of thought.
However, she has been secretly replaced by Mystique.
In the cinematic/TV universe (Earth 199999)
The primary reason behind the separation is, as others have pointed out, an issue of rights. Rights to all mutant franchises and references to them, as well as the Fantastic Four and are owned by Fox, while Marvel holds rights to S.H.I.E.L.D and the Avengers and related properties (and Sony still owns rights to the Spider-Man). As such, the mutants do not currently exist in the Marvel Cinematic Universe - with a small pseudo-exception of Quicksilver and Scarlet Witch, who will not be mutants in the MCU.
Beyond that, a distinction must be made in regards to being a member of S.H.I.E.L.D, and a member of the Avengers. Currently, in the MCU, no super-powered being exists as a member of S.H.I.E.L.D - only as a member of the Avengers (remember that Black Widow and Hawkeye are merely highly trained agents with exceptional abilities).
Edit: The recent Captain America: The Winter Soldier trailer mentions Cap saying that he "joined S.H.I.E.L.D" at some point. Exactly when this happened is unclear. He worked with/for them during The Avengers, but I never got the impression that any of the Avengers aside from Black Widow and Hawkeye were official agents.
During the course of The Avengers movie, the council which governs S.H.I.E.L.D shows disapproval of counting on super-powered beings. While Director Fury and his men on the ground may be OK fighting alongside the Avengers, it is entirely possible that S.H.I.E.L.D's governing body may restrict super-powered beings from being actual agents of S.H.I.E.L.D.
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