There are two responses for this. One leans heavily on a story once told by the late Rev. Billy Graham that MacArthur didn't think a top-down imposition of religion would be legitimate or effective and Christianity would need to be adopted by the population voluntarily (it's possible to question the veracity of the anecdote as it relates to the Emperor). To that end he requested thousands of missionaries, got barely one thousand (peace meant that there was demand again for missionaries all over the world, not just Japan), and the efforts petered out eventually. In other words, he tried as hard to Christianize Japan as he could in good conscience. Ray Moore's Soldier of God basically takes this perspective.

The other response is that he bloody well did. The nation wasn't fully Christianized and only about 2-3% of Japanese today identify as Christian, but

• the State Shinto system was dismantled almost immediately after armistice (by MacArthur)
• more than 60% of Japanese currently identify as "not religious" and fewer than 10% are members of any organized religious group
• a number of Christian junior colleges, seminaries, and universities were founded or refounded after the war
• six Christians have served as Prime Minister of Japan since the end of the war (out of 31 total)
• most of the wedding ceremonies (possibly as many as 70%) that now take place in Japan are Christian, rather than Shinto, Buddhist, or secular

To my mind that's too impressive a list of accomplishments to call "no significant headway." If nothing else, Christianity is at least as normalized as Buddhism or Shintoism in contemporary Japan, maybe a little bit more.