The Greek Catholics are the descendents of the Orthodox of Carpatho-Rus, called Ruthenians by the Latins, 'Rusyn', 'Rusin' or Carpatho-Russian by some of them today and are Greek Catholic as a result of the Union of Uzhorod. They are within the Eparchy of Presov with a Diocese in Kosice. Transcarpathia, i.e.the Eparchies of Mucachevo and Uzhorod, was part of the Austro-Hungarian Empire and the nation of Czechoslovakia prior to World War 2 and was ceded to the USSR and annexed to Ukraine pursuant to the agreements at the Potsdam Conference and the end of the war.
Within both the USSR and Czechoslovakia, the Greek Catholic Church was 'liquidated' in 1947 by the Communists. It should be noted that the Greek Catholics in Slovakia were not impacted by the anti-Greek Catholic attitude among the Latin clergy and hierarchy that they faced in America, nor was forced celibacy ever attempted by Rome in these regions in modern times.
Following the 'Prague Spring' in 1968, the Greek Catholic Church was revived in Czechoslovakia and the majority of the Eastern Christians returned to outward Greek Catholicism. After the fall of the USSR and the independence of Ukraine in the early 1990's, the same occurred within Transcarpathia and western Ukraine.
While Orthodoxy has maintained a foothold in both Slovakia and the Czech lands, the simple answer to the OP's question, IMHO, is that Orthodoxy was associated with Russia, the historic enemy and occupier of these regions. Unfortunately, the behavior of many of the emissaries of the Church of Russia did little during the post-Hapsburg years to dispel that association.
Prior to the war, the Orthodox had a more vibrant presence in the regions around Prague due to the relocation of Russians following the Revolution and the Civil War. In Slovakia, the Orthodox maintained a pre-war presence in and around Ladimirova as a result of the Russian Church in Exile locating in that area, it was the home village of the late Metropolitan Laurus of ROCOR. Today the Orthodox community is small, but vibrant, and maintains the traditional praxis and hymnology of the Rusyn people.
Orthodox Website from Presov Diocese: http://http://www.orthodox.sk/
Greek Catholic Website from Presov: http://www.grkatpo.sk/