U.S. special Middle East envoy Philip C. Habib met with Syrian President Hafez Assad in Damascus today as thousands of residents demonstrated in the streets of the Syrian capital to protest a bomb explosion Sunday that killed scores of people.

Despite a spate of attacks in the Arab press against the United States for its conclusion of a strategic cooperation agreement with Israel early this week, today's meeting in Damascus which concentrated on the situation in Lebanon was termed "warm and friendly" by a U.S. spokesman.

That was not the mood of the demonstrators who, at government instigation, turned out in the streets of the capital as the meeting between Habib and the president was going on in the Mohajereen Palace. The demonstrators chanted their protests against the explosion of a car bomb in the capital's Azbakiyah district Sunday that destroyed four buildings, killed scores of people and wounded as many as 150, many of whom have since died in hospitals.

The Syrian government kept its official comments on the meeting to a minimum stating only that the talks had been "about the situation in Lebanon and about ways of establishing national reconciliation in Lebanon."

The government has blamed the bomb blast, the latest of four in the capital in recent months, on the fundamentalist Moslem Brotherhood, which has been waging a violent underground campaign against Assad's Alawite-sect-dominated government for the past 2 1/2 years.

Although Assad's government maintained a formally correct attitude toward Habib's fourth mediation mission in the area this year, the crowds in the street shouted anti-American slogans and repeatedly termed the Moslem Brotherhood "agents of Israel," reflecting previous Syrian press statements that implied there was a link between Habib's mission and the exploding car bomb.

Habib arrived in Damascus Monday after a drive from neighboring Beirut where he had launched his new mission with a series of talks with Lebanese leaders. Opening his meeting with the Syrian president today, he delivered a note from President Reagan expressing "deep regrets" over the bombing. The note stated "such wanton taking of innocent lives cannot be justified for any reason. We express our abhorrence to acts of terrorism anywhere."

There was no indication, however, that Habib made any significant progress on his basic mission to reinforce the cease-fire between Israel and the Palestine Liberation Organization in southern Lebanon, which he had negotiated last summer. He originally came to negotiate the cease-fire last April, then has remained involved in efforts to induce the Syrians to withdraw SA6 antiaircraft missiles that they installed in Lebanon's Bekaa Valley after Israeli planes shot down two Syrian troop helicopters in the area last spring.

Israel has repeatedly urged the United States to push the Syrians to remove the missiles -- or face the possibility that Israel will take it upon itself to knock them out.

Arab and Western diplomats in Beirut today had little hope that Habib would succeed in persuading the Syrians to remove the missiles given the fact that he has little inducement to offer President Assad for their removal.

Habib is expected to fly to Saudi Arabia Thursday. He will also visit Israel, and a delegation spokesman said today he had added Jordan to his itinerary.