Rumors had persisted then that the Maitatsine received aid from Nigeria's elite, but became too much for politicians to control. Similar rumors now surround Boko Haram, which wants the strict implementation of Shariah law across Nigeria, a nation of more than 160 million split largely between a Christian south and Muslim north.
Other analysts suggest Jonathan, a Christian who took power after the 2010 death of an elected Muslim leader, remains unsure of his grip on the nation. The April election that saw Jonathan cement his hold on the presidency also sparked political and religious rioting across Nigeria's north that left 800 people dead.
Boko Haram's name means "Western education is sacrilege" in the local Hausa language. It rejects Western ideals like Nigeria's U.S.-styled democracy. Followers believe that democracy has destroyed the country with corrupt politicians.
The latest attacks occurred ahead of Sunday's celebration of the feast of sacrifice, when Muslims around the world slaughter sheep and cattle in remembrance of Abraham's near-sacrifice of his son.
An Associated Press count shows the group has killed at least 361 people this year alone.
Associated Press writer Njadvara Musa in Maiduguri, Nigeria contributed to this report.
Jon Gambrell can be reached at www.twitter.com/jongambrellAP.