The government of Jordan has been a "loose" ally of the US dating back to the first Gulf War. The following may help shed light on why Al Quaeda would want to attack Jordan government and military targets (and an American Embassy there):
In January [2003], Jordan received six U.S. F-16s to strengthen its defense, and has been promised up to 11 more. Additionally, anywhere between "several hundred" and 2,000 U.S. troops are currently stationed in Jordan to operate newly delivered Patriot anti-missile systems and coordinate search-and-rescue missions in Iraq. In October 2002, 1,000 U.S. soldiers began to train in the Jordanian desert with other troops from the region. Jordan's position this time around varies greatly from the neutral position it held in the 1991 Gulf War. And while King Abdullah has refused to directly assist the United States if it invades Iraq, indications point to Jordan's active support for the United States thus far being rewarded with additional military assistance. Jordan received $350 million in U.S. military aid in FY 02 and has been promised an increase of $100 million this year. Jordan has requested up to $1 billion in aid to defray the cost of a potential flood of Iraqi refugees.
Also:
Egypt has also asked for a free-trade deal similar to the one Jordan negotiated with the United States after actively supporting U.S. efforts in Afghanistan.