There is some pretty solid primary source documentation that addresses your question. Let's start with a brief U.S. government memorandum: http://www.mediafire.com/view/6t3x18rfb2yd0ln/United_States_Initial_Post-Surrender_Policy_for_Japan_SWNCC15.pdf

This is an internal government document that essentially lays out the broad tenets of U.S. policy towards post-surrender Japan. We know this because, well, that's what the document says:

This document is intended as a statement of general initial policies relating to Japan after surrender. Following Presidential approval, it will be distributed to appropriate United States departments and agencies for their guidance.

Now with respect to your actual question—this document provides a fairly basic justification for the retention of the Emperor in post-surrender Japan. Doing so simply represented the path of least resistance to accomplishing U.S. goals:

In view of the present character of Japanese society and the desire of the United States to attain its objectives with a minimum commitment of its forces and resources, the Supreme Commander will exercise his authority through Japanese governmental machinery and agencies, including the Emperor, to the extent that this satisfactorily furthers United States objectives [emphasis mine].

The document also clarifies that the Emperor is to serve merely as a figurehead for U.S. authority:

This policy, however, will be subject to the right and duty of the Supreme Commander to require changes in governmental machinery or personnel or to act directly if the Emperor or other Japanese authority does not satisfactorily meet the requirements of the Supreme Commander in effectuating the surrender terms.

And finally, the document very succinctly recaps the rationale for carving out a continued role for the emperor in a transitory period for Japan:

This policy, moreover, does not commit the Supreme Commander to support the Emperor or any other Japanese governmental authority in opposition to evolutionary changes looking toward the attainment of United States objectives. The policy is to use the existing form of Government in Japan, not to support it [emphasis mine].

Why did U.S. policymakers see the Emperor as key to implementing U.S. objectives? This mostly has to do with the perceived centrality of the Emperor to the authority and legitimacy of the Japanese regime. For example, pre-war Japanese documents such as Cardinal Principles of National Polity articulated an ideology that located the emperor as a divine being located at the center of the Japanese people.

Note that I use and emphasize the term "perceived" because the presumption that all Japanese people revered the Emperor to such an extent that they would resist his toppling and fight to the death is incorrect. In fact, I wrote a paper in one of my undergraduate classes on this very subject, which I highly encourage you to read (no works cited included, but I can dig it up if there's demand).

But onward with the meat of our discussion: ideological revisionism notwithstanding, the preservation of the Emperor was still a significant factor in Japan's surrender. That is to say that even if Japanese citizens were ambivalent about the continued role of the Emperor in society, those who directly operated around the Emperor were much more invested in his preservation. In fact, as Eiji Takamae describes in Inside GHQ: The Allied Occupation of Japan and its Legacy, the surrender itself was so contingent upon this question that it required something of a happy accident:

On 10 August (Tokyo time), at Hirohito's insistence, the Suzuki Cabinet tentatively accepted the Potsdam terms on condition that the Allies vouchsafe the Imperial institution and its 'prerogatives'. On 11 August (EST), Secretary of State Byrnes issued a purposely vague communique stating that the authority of the Emperor and government would be subject to the Allied Supreme Commander but suggesting that the monarchy would not be overthrown unilaterally. To quell angry opposition from the Army and war faction, Foreign Ministry translators doctored the language of the Byrnes Note to convey the impression of an Allied commitment to Imperial sovereignty, and on 14 August, again at Hirohito's prompting, Tokyo formally agreed to capitulate, ending days of tense and convoluted deliberations (Takamae 46).

Finally, I should point out that the Emperor's retention was not a spontaneous decision; it was the culmination of many months of carefully orchestrated maneuvers that MacArthur and his subordinates initiated in preparation for an invasion of Japan. The goal of these maneuvers was to partition the Emperor from the rest of the government in order to more readily assure the cooperation of the Japanese people. As Eiji Takamae explains:

In June 1944, as preparations for the invasion intensified, MacArthur created the Psychological Warfare Branch (PWB), SWPA and assigned his military secretary, Major Bonner Fellers, to direct its operations. Fellers was convinced that Allied propaganda could succeed only by telling the truth. At the same time, he directed the PWB to avoid direct criticism of the Emperor, who was to be portrayed as a victim of the militarists and used to achieve peace. Japanese military documents suggest that this approach was surprisingly effective in spreading doubt and disaffection among the rank-and-file as Japan's battlefront position grew desperate (Takamae 18).

Hope this helps!

Primarily because MacArthur needed help ruling 80 million Japanese with pacification forces which were inadequate to rule without the cooperation of the Japanese people. There were powerful men in Washington who did want Hirohito tried, but there was no consensus, and MacArthur took advantage of that and shielded Hirohito for pragmatic reasons. Source: Partners for Democracy: Crafting the New Japanese State Under MacArthur by Ray A. Moore and Donald L. Robinson, Oxford University Press, 2004.