The government has an awkward situation in Syria. Immediately after the April 7 American cruise missile attack on a Syrian air base (in retaliation of earlier Syrian use of nerve gas) the Russian Internet lit up with embarrassing discussions about that happened to Russian boasts in late 2016 that the Russian air defense system in Syria was operational. Using these very current and high-tech air defense weapons (Tor 2, S-400 and so on) Russia controlled who could use Syrian air space. Thus the American use of 59 cruise missiles to hit that Syrian air base, destroy about 20 percent of the Syrian air force and not touch the Russian aircraft and troops there, was either done with Russian permission or these expensive new air defense systems were vulnerable to American countermeasures. That was a common source of humiliation during the Cold War when, time and time again, the West, usually the Americans, came up with some unexpected tech to neutralize Russian systems, especially air defense and aircraft electronics. The government was forced to note these embarrassing comments on Russian language Internet message boards and announced that Russian policy was not to use the air defense system against external air threats in Syria, or at least not the ones that were no threat to Russian troops. Other government officials commented that the Russian air defense systems could detect low-flying cruise missiles but not everywhere as these cruise missiles could be programmed to deliberately take advantage of terrain (hills) and also detect and avoid Russian radars. Older Russians then recalled hearing the same excuses during the Cold War. The people running Russia remember it as well and that seemed to account for the public displays (in the UN and to the international media) of anger at the Americans. It wasn’t just what the Americans did but how they did it.Russia has more to dislike about what the U.S. is doing in Syria. For example there are the bases the Americans are building in northern (Kurd controlled) Syria. Turkey and the Assads oppose these American bases but the bases remain because the Americans, and most of the world, no longer consider the Assads legitimate rulers of Syria. The Assads and their allies Iran and Russia disagree. As long as the American bases were there to support the fight against ISIL (Islamic State in Iraq and the Levant) Iran and Russia did not make an issue of these bases or the thousand or so U.S. troops in Syria. But now that the U.S. has, for the first time, carried out a major military attack on the Assad forces and may continue to do so, a suitable response is necessary. There is not much the Assads can do. They have not been able to prevent regular Israeli air attacks (to prevent Iranian advanced weapons from being moved to Lebanon) and it is no secret that the U.S. and Israel are close allies. The Russians have already made it clear that they will side with the Israelis if forced to decide between the Assads and Israel. This has put Iran in a difficult position and the latest American move makes that worse. All foreign forces operating in Syria are supposed to be there to deal with ISIL but Iran and Russia only pretended and were often criticized because most of the military activity in Syria was to weaken rebels (mainly non-ISIL) fighting to overthrow the Assads.
While Russia is officially in Syria to defeat ISIL and keep the Assads in power they (semi-officially) also want to maintain good relations with Israel and Sunni Arab countries while doing it. This annoys Iran. Israel has made it clear that there can never be peace in Syria if Iran tries to establish a permanent presence there. The Iranians say they are in Syria to stay and the Russians (so far) have said they oppose that. Iran wants to stay in Syria as part of its decades old effort to destroy Israel and a centuries old effort to make the Shia form of Islam dominant in the Islamic world (that is over 80 percent non-Shia). Meanwhile Israel says it can live with the Assads as long as Iran is not maintaining a military presence in Syria. Many Turks agree with Israel on that point and newly elected U.S. government has come out strongly against any permanent Iranian presence in Syria. The Americans still want the Assads gone but despite that the U.S., Israel and Turkey agree on some key goals.
The Russian intervention appears to be permanent (as far as the Russians are concerned) and the Assads are OK with that. Turkey and Iran are not so sure and Iran is openly opposed to Turkish troops being in Syria at all. At the same time Iran is demanding the right to establish a naval base in Syria. This is not a new idea. In 2011 Iran pledged to pay for the construction of a naval base on the Syrian Mediterranean coast. That proposal was put aside as the rebellion against the Assads grew but now Iran wants some payback for playing a key role in maintaining the Assads in power. All these overlapping and often contradictory goals and alliances may seem odd to an outsider but this is the Middle East, where such complex arrangements are the old normal.