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MOSCOW — The champagne toasts that some Russian officials quaffed just a few short months ago to celebrate the victory of Donald J. Trump have gone a bit flat.

Euphoria was already starting to cede to caution before Michael T. Flynn, President Trump’s national security adviser and a perceived friend of Russia, resigned. That cemented the uneasy mood.

The departure of Mr. Flynn on Monday over his contacts with the Russian ambassador to Washington was the latest in a series of mixed signals from Mr. Trump and his advisers on a host of issues important to Russia, particularly the lifting of economic sanctions.

Now, many prominent political figures are wondering whether hopes for change were premature, and whether Moscow will inevitably remain Washington’s main boogeyman. On Tuesday, the Pentagon was confrontational, accusing Moscow of secretly deploying a cruise missile system that violates a 1987 treaty on intermediate-range missiles based on land.

Vladimir R. Soloviev, the host of a noisy Sunday night talk show on state-run television viewed as reflecting Kremlin policy, this week issued one of the most negative public assessments yet of Mr. Trump. “Don’t be charmed by Trump,” he said in a message he addressed to all politicians and experts. “Don’t think that Trump is a pro-Russian politician. Don’t hope that Trump, in the interests of Russia, will in any way go against the basic, rooted interests of America.”

How things have changed since November, when the Russian Parliament greeted Mr. Trump’s election with a round of applause and a prominent political leader — albeit one famous for his antics — toasted the victory with champagne on national television. In January, Mr. Trump garnered more mentions than President Vladimir V. Putin in the Russian news media, knocking the Russian leader from the top spot for the first time since 2011.

Only one man, Mr. Putin, really sets Russia’s foreign policy course, however. And he was never publicly celebratory, although his animosity toward Hillary Clinton, whom he blamed for the angry demonstrations that greeted his return to the presidency in 2012, was well known.

In recent years, Mr. Putin’s main foreign policy goal has been to resurrect the time when the United States and the Soviet Union, as the two great nuclear superpowers, were the main arbitrators of the global order. Lacking the might of the Soviet Union, Mr. Putin has tried to punch above his weight by shocking the world with unexpected tactics like seizing Crimea, destabilizing Ukraine and deploying his military in Syria to shore up President Bashar al-Assad.

President Barack Obama responded by referring to Russia as a declining regional power. The two men had a poisonous personal relationship.

Mr. Trump seemed to presage a different era with all the praise he heaped on Russia and Mr. Putin. He described him as a strong, smart leader and said that Moscow seemed to be blamed for everything. And he called for better relations with Moscow to fight the Islamic State and other terrorist groups, echoing a longstanding Putin pitch.

Some voices in Moscow cautioned that Mrs. Clinton, as a calmer hand on the tiller, would be the kind of predictable leader that the Kremlin preferred, albeit a hostile one. Now, there is a sense that the Kremlin might be unsettled by the president of a far more powerful country deploying Mr. Putin’s favorite tactic: unpredictability.

“Trump will be tamed and act more presidential, eventually, but he also has a penchant for unpredictability that works against the Kremlin,” said Konstantin von Eggert, a political commentator for TV Rain, Russia’s only independent channel. “This creates a situation in which a stronger player with the same style of unpredictability as a strategy comes on the stage. Putin did not anticipate that.”

There has been a certain amount of policy whiplash on issues important to Russia. First, Mr. Trump said that NATO was obsolete, then that it had America’s solid backing. He seemed to indicate he would lift economic sanctions imposed over the Ukraine crisis, and appointed as secretary of state Rex W. Tillerson, who as head of Exxon Mobil cut enormous oil deals with Russia and spoke out publicly against sanctions.

Then the new United States ambassador to the United Nations, Nikki R. Haley, sharply criticized Russia over Ukraine, suggesting that sanctions were hinged to a peace deal there. Mr. Tillerson echoed that line.

Finally, Mr. Trump started to mix geopolitical apples and oranges, crossing issues in a way that Moscow deplores. He said maybe sanctions could be lifted in exchange for a better deal on nuclear arms. The Trump administration seemed to want the Kremlin to distance itself from Iran, its ally in Syria, and from China.

“There is a cautious feeling about how Trump and his advisers designated the possible ways of improving relations with Russia,” said Vladimir Frolov, an international affairs analyst. “This has frightened the Kremlin because it does not correspond to Russia’s interests.”

The idea that Mr. Flynn was forced to resign over contacts with the Russian ambassador, Sergey I. Kislyak, fed the suspicion that relations with Moscow were the main target and that Russophobia was again stalking Washington. Accusations that Russia interfered in the American elections have generally been dismissed on these grounds.

Since Mr. Trump’s victory there has also been a quiet drumbeat in Moscow, where conspiracy theories are never far below the surface, that the American establishment would overthrow him.

“Either Trump has not found the necessary independence and has been driven into a corner,” wrote Konstantin Kosachev, the head of the international affairs committee in the upper house of Parliament. “Or Russophobia has permeated the new administration from top to bottom.”

Alexei Pushkov, another lawmaker, said on Twitter that after Mr. Flynn, Mr. Trump himself might be the next target.

Dmitry S. Peskov, the spokesman for Mr. Putin, declined to comment on Tuesday about the resignation, calling it an internal American affair. Just last Friday, in an evident attempt to help Mr. Flynn, Mr. Peskov had denied that the American official and the Russian ambassador had discussed sanctions. In resigning, Mr. Flynn conceded that they had.

Mr. Peskov called it premature to predict the course of Russian-American relations.