President Reagan's brief stopover here Saturday, hailed as an endorsement of democracy, also spotlights the tight Honduran military cooperation with U.S. policy in Central America that reportedly has generated friction between the civilian and military leadership here.

The United States has promoted democratic institutions producing the first elected Honduran government in a decade, but an officer corps grown accustomed to unfettered power through military coups is closely identified with a U.S. campaign against the revolutionary government in neighboring Nicaragua.

"Why is Reagan coming here?" asked Guillermo Perez, dean of the National Autonomous University law school. "Is he coming here to show support for our democracy, or to toss his fighting cock into the pit and cry, 'This is my rooster'?"

The military-civilian alliance has seemed particularly strained in recent weeks, informed Honduran sources say.

Foreign Minister Edgardo Paz Barnica has been the cutting edge in a three-week effort by the civilian government to reach peaceful accommodation with Nicaraguan leaders, who accuse Honduras of harboring counterrevolutionary guerrillas in cooperation with the United States and preparing them for an invasion.

But according to sources close to the minister, he has encountered opposition from the armed forces commander, Gen. Gustavo Alvarez Martinez. The general has declared Honduras is locked in a "war to the death" with Nicaragua's Sandinistas, whom he equates with "international communism." He called for a military alliance grouping El Salvador, Guatemala and Honduras against Managua.

"One thing is what the government wants to do; another thing is what the Army wants to do," said Efrain Diaz Arrivillaga, the lone Christian Democratic opposition member of the 82-member Congress.

Although President Roberto Suazo Cordova's government was elected Nov. 29, 1981, in what even his opponents qualify as honest balloting, the Army remains a strong political force--with its history of five coups since the mid-1950s hanging like a cloud over elected rulers.

"The civilian government is afraid and feels it has to keep the Army happy to keep safe," a former minister said. "It is what we call taking care of their seats."

Rightly or wrongly, what the Army wants to do is often interpreted here as what the United States wants to do. U.S. military aid to the Honduran armed forces has doubled in one year to more than $10.5 million for 1982. The Reagan administration has outlined requests of about $60 million for 1983-4. At least 40 U.S. advisers help train the Army and Air Force. At the same time, the Army has intensified border patrols to choke off Nicaraguan aid to Salvadoran guerrillas and backstopped offensives by the Salvadoran Army, both in line with U.S. objectives.

"What we fear is that the United States and U.S. Ambassador John D. Negroponte view Honduras only in the perspective of what is happening in El Salvador and Nicaragua," Diaz said. "The United States is using Honduras. We are a card to play to get a grip on Nicaragua, as part of its policy of destabilizing Nicaragua."

Illustrating the point, activist lawyer Gautama Fonseca pointed out that the United States plans to spend $21 million to improve airfields in Honduras and Colombia for military use while Tegucigalpa's international airport remains unfit to handle Reagan's Air Force One safely, forcing him to land in San Pedro Sula instead of the capital. The three Honduran fields to be lengthened for military use are all near the Nicaraguan border.

After what a former minister, who remains close to Paz Barnica, called a "hot point" of tension in mid-November, the tide now appears to be flowing in favor of attempts at accommodation. The foreign minister visited Managua on Nov. 12. Four days later, Suazo Cordova's government issued a communique pledging to control its border with Nicaragua.

In the meantime, counterrevolutionary camps have been dismantled in several spots along the border and a formerly reluctant Army has agreed to help move Nicaraguan refugee camps 30 miles from the frontier. Alvarez has declared there are no guerrilla camps on Honduran soil and has gone out of his way recently to emphasize military subordination to elected civilian leaders.

It was a measure of political life here that his statement on the subject was page one news in local newspapers. Acording to well-informed and impartial sources, Alvarez has not written off Honduran aid to the Nicaraguan rebels and maintains the power to alter policies. "I think the minister of foreign affairs is full of good intentions, but this is not the only thesis in Honduras," said Carlos Roberto Reina, a politically active lawyer who describes himself as left of center. "We have two foreign policies."