First, Macbeth says, "If it were done when 'tis done, then 'twere well / It were done quickly."  In other words, if simply killing Duncan would conclude the whole affair and render Macbeth king, then he would go ahead and do it now.  However, a lot will have to happen in between the murder and his coronation: he will have to lie to his friends, act as though he is aggrieved and shocked by the crime, and perhaps even engage in some political jostling with Duncan's sons.

Next, he expresses his knowledge that the consequences of this murder will have to be resolved. The murder itself will not neatly conclude by itself; otherwise, he would be willing to risk everything, including his soul's time in the afterlife, to get the murder finished.

Then, he suggests that he will "teach / Bloody instructions" that could "return / To plague th' inventor."  What he means is that, in committing such a violent crime, he will inadvertently show others that one can commit such a crime and get away with it.  If he kills Duncan, then it stands to reason that someone could turn around and kill him next!

Next, he considers that he is both Duncan's "kinsman," or family member, and "subject," as the king ranks above him.  Further, he is Duncan's "host," which means that he should be fighting to keep anyone wishing Duncan harm at bay, not considering murder himself.  

After this, he reflects on Duncan's virtues and his goodness as a king, saying that he has been "So clear in his great office."  Duncan has been humble and honest, so people everywhere will grieve for his loss.

Macbeth realizes that killing the king will have several consequences. He realizes that his soul will be damned for the murder and he will pay a very harsh price in the afterlife. In addition, the murder of the king will only cause more violence, some of which will be directed at Macbeth because one, he is the murderer, and two, he would now be the king.
In addition to these consequences, Macbeth recognizes that Duncan has been a good king and has shown Macbeth nothing but respect. In fact, Duncan has just rewarded Macbeth with the title of Thane of Cawdor. Macbeth realizes that the only reason he has to kill the king is his own ambition. So, as a subject of the king and as his host while Duncan visits, Macbeth should protect the king from harm, not do harm to him.

Macbeth says that he should not kill Duncan because they are related, because Duncan is his king, and because he (Duncan) is Macbeth's guest, and as host Macbeth should protect him. He also says that there will be justice against such an action, as well as simple revenge. (Someone might kill him the same way.) Since Duncan is in this situation good and innocent, even angels might cry out against the crime. Everyone will find out, Macbeth says, and what makes it worse is that he doesn't really have a valid reason for killing Duncan.