Why wasn't the 1953 Iranian coup d’état considered to be a violation of United Nations Charter?

Because the United States of America is "special". It does not need to (want to?). Why? Presumably because they are special!.

First, because they plotted the coup (and also because they have never followed public international law -- commentary of Professor Murphy below).

So, because of this:

CIA Confirms Role in 1953 Iran Coup

Documents Provide New Details on Mosaddeq Overthrow and Its Aftermath

National Security Archive Calls for Release of Remaining Classified Record

National Security Archive Electronic Briefing Book No. 435

Posted – August 19, 2013

Edited by Malcolm Byrne

SOURCE: The National Security Archive (The George Washington University)

Foreign Policy has a short write-up. Here's an excerpt:

TPAJAX was the CIA’s codename for the overthrow plot, which relied on local collaborators at every stage. It consisted of several steps: using propaganda to undermine Mossadegh politically, inducing the Shah to cooperate, bribing members of parliament, organizing the security forces, and ginning up public demonstrations. The initial attempt actually failed, but after a mad scramble the coup forces pulled themselves together and came through on their second try, on August 19.

Why the CIA finally chose to own up to its role is as unclear as some of the reasons it has held onto this information for so long. CIA and British operatives have written books and articles on the operation — notably Kermit Roosevelt, the agency’s chief overseer of the coup. Scholars have produced many more books, including several just in the past few years. Moreover, two American presidents (Clinton and Obama) have publicly acknowledged the U.S. role in the coup.

SOURCE: CIA Admits It Was Behind Iran’s Coup (2013/08/19)

Additional information requested (from comments - see below).

The United States and the International Court of Justice: Coping with Antinomies

(page 2)... the United States operates on the basis of conflicting principles with respect to whether states should be treated as equal sovereigns or as units characterized by inescapable power differentials. While the United States historically has articulated a desire for cooperation with other states as co-equal sovereigns — and, indeed, has been in the vanguard in many respects in the promotion and development of international law and institutions built around the concept of sovereign equality — the United States has innate historical and cultural characteristics that push it toward an attitude of “exceptionalism” in its foreign policy, claiming itself entitled, formally and informally, to be treated differently from other states.

(page 55) For Europeans, the concept of a supra-national court reaching decisions that directly affect the lives of individuals is nothing new; the European Court on Human Rights has existed for almost fifty years, and has handed down hundreds of cases that reach deeply into the national legal systems of EU member states. Likewise, the European Court of Justice reaches directly into national legal systems in various ways. Regional human rights courts in the Americas and now in Africa have a less strong pedigree, but nevertheless, for states adhering to their jurisdiction, the concept of such supra-national adjudication as having effects on internal decision-making is understood. For Americans, however, there is no such tradition of allowing intrusion into the U.S. legal system (for example, the United States has never accepted the jurisdiction of the InterAmerican Court of Human Rights).

SOURCE: Sean D. Murphy, The United States and the International Court of Justice: Coping with Antinomies in THE UNITED STATES AND INTERNATIONAL COURTS AND TRIBUNALS (Cesare Romano, ed., 2008)

Professor Murphy is professor of Public International and U.S. foreign relations law at George Washington University. Article available (pdf).