There are several reasons for this. First, we have to remember why we still remember Franklin and Jefferson in regards to the founding of the nation. Jefferson is the one who wrote the first draft of the Declaration of Independence. He also became president and presided over the Louisiana Purchase. He had a very memorable career and strong public support. Franklin was a famous inventor and international figure, going abroad to secure money. These men had very colorful lives and personalities and relatively small amounts of scandal in their career. Jefferson was a contentious figure because of the rise of party politics, but there was never anything that soured the whole nation against him. Franklin also achieved this status with his famous personality and wit. Adams suffered from a very prickly disposition. He did not get along well with other. His work is also somewhat harder to pin down. He didn't write the Declaration like Jefferson or the Bill of Rights or anything that is directly used. He was a major player in bringing about Independence, but he is harder to attribute specific accomplishments to. But I personally think a major part of our ignorance about him comes from the Alien and Sedition Acts. These acts made writing against the government a crime. America was sort of at war with France at the moment without it ever being declared. When the "war" finished, congress was worried about the influence of foreign powers in the very young country. They passed acts requiring foreigners to be in the country longer to become citizens and forbade speech critical of the government. Adams signed them when Congress passed them. As usual, the president took the rap for what congress did while the congressmen get nothing. He lost his reelection bid and no one paid attention to him anymore. His reputation was rather soured.

I recommend McCullough's book John Adams for more information.

I actually wrote my undergraduate dissertation on this exact topic. Adams himself felt under appreciated at that time, once saying: “The essence of the Revolution will be that of Dr. Franklin’s electrical rod smote the earth and out sprung General Washington. That Franklin electrified him with his rod – and thence forward these two conducted all the policy, negotiation, legislatures, and war.”