Actually, if you look carefully at the text, Shylock is very careful to say that the pound of flesh could be cut from wherever he chose. Therefore, in theory, he could have chosen to cut out the heart of Antonio. If we look back at Act I scene 3 which is an important scene for many reasons, we see the exact terms of the "merry bond" that Shylock draws up with Antonio:
...let the forfeit
Be nominated for an equal pound
Of your fair flesh, to be cut off and taken
In what part of your body pleaseth me.
So therefore, whilst Shylock does not specify which part of the body he will take as forfeit, he could have, in theory, chosen to cut out the heart of Antonio as his pound of flesh. I suppose we need to think about Shylock's motivation in answering this question. He is after revenge for the wrongs that Antonio has committed against him and his race, and thus his desire is to cause pain, to mutilate, and perhaps to kill.
A brief answer is in keeping with comments from G. B. Shaw and Marchette Chute: Shakespeare as storyteller. He was following his sources. Beyond that, one can go in various directions. Shylock's "flesh of mutton's, beefs or goats" (1.3) and Antonio's "I am a tainted wether of the flock(4.1) allow Professor Garber to provide an interesting explanation of chapter 16 from LEVITICUS(see her SHAKESPEARE AFTER ALL, page 309). As I have suggested(see discussion board), the play is linked throughout with ROMEO AND JULIET. Therefore, one might note "O nature, what hadst thou to do in hell / When thou didst bower the spirit of a fiend / In mortal paradise of such sweet flesh?"ROM3.2) and "O, here / Will I set up my everlasting rest / And shake the yoke of inauspicious stars / from this world-wearied flesh"(ROM5.3). Shylock's "I will have the heart of him if he forfeit"(MV3.1) is more directly linked to the question but I have to go for now.