Shoulder mounted anti air weapons (MANPADS) have a very limited range, and are most effective against slow & low flying airplanes and helicopters. A bomber with an altitude of 12km is not exactly affected by them ( but is affected by other anti air systems). Air superiority and air defence is a very complex topic with many inter-movable parts and entire libraries have been written about it (and considering the war in Ukraine and other potential hotspots new libraries will be written).
A very small summary of some points to consider.
You have multiple layers of air defence, from short to long range, with different advantages and disadvantages.
Every war is heavily depending on the economic ability to sustain such a war and on the military structure and logistics to support your front.
War is rarely the Hollywood battle with the one decisive battle and epic music, where everything is resolved. Many, perhaps most wars, are in the end battles of small victories (hopefully for your side) and losses (hopefully for the enemy) and the attempt to drain resources from the enemy faster than the enemy drains it from you.
With that you attempt to identify the enemies structure and logistics. From small and large radar to maintenance facilities (for airplanes) and of course where enemy airplanes are gathered, hidden. You check what kind of air doctrine the enemy has and how he will attempt to implement it. You update your own war planes to counter the enemy attempts and push forward your own goals.
A "classic" air war would be to destroy enemy airplanes, airports, secondary bases (like specially build roads in Finland for off-site emergency runways), radar stations (mobile and stationary) and maintenance facilities for complex aircraft parts (storage, production, transport of these sytems), you hunt down SAM launchers if the occasion arises, you disrupt enemy communication and control centres. You attempt to draw out hidden enemy forces so that you can actually find and destroy them. If the enemy has an integrated air defence network system (a system where many different systems, land/air/sea, short- to long range are integrated into one system distributed over large areas of the battlefield), this will take a lot of resources, losses and time.
"Destroying" does not always mean destroying it physically. It can very mean that the enemy is forced to reduce his resources, distribute them to cover a larger area or have to retreat them in order to preserve them. An example would be the war in Ukraine: while a large part of the Ukrainian air defence structure and the air force was destroyed in the opening stages of the war, the Ukrainian forces were forced to retreat and/or hide their remaining system and to adapt their remains to the abilities of the Russian attacks. With that and the slow regeneration of some of their abilities due to foreign military help they were finally able to deny full air dominance to the Russian forces ... while on the other side the destruction of the Moskva cruiser forced the Russian Black Sea Navy to retreat as they suddenly lost a major part of their long range anti air protection bubble. With that the Ukrainian Air Force had suddenly a bit breathing space and could increase their operations a bit.
In the end: a game played in the fog, with all participants are half blind and where the first person who activates the flash light gets some nasty hits.
SYL