The vast majority of Estonians (including politicians, military) considered the German ruling class as the enemy.
The question is, why did the Estonians hate the ethnic German minority, and consider it as the enemy, and was that feeling rational, or rather self-defeating.The German landowners were hated by 99% of Estonians. There was huge need of land amongst the peasants. The Estonian government promised to take the land from the Germans and give them to the Estonians. This was the driving force of the Estonian Republic - soldiers fought for being in their own state with their land.
No doubt, Reigo, you and other Estonians consider Estonia to be a Western country, quite different from its neighbour Russia. Latvians feel the same way. And from what I have read, and from what I have heard people who have visited the two countries say, both Estonia and Latvia appear very Western in terms of appearance and culture.
But what gave Estonia and Latvia their Western culture and orientation? It was the Germans who settled in those countries and developed them. Without the German settlement, both Estonia and Latvia would have ended up as Eastern countries like Russia, or as quasi-Western countries like Lithuania and Poland.
By expropriating and marginalising the ethnic German minority, the new Estonian and Latvian middle classes effectively destroyed the most Western element in their societies. In a way, they were acting much as Zimbabwe is today.
The most cursory examination of the history of the 19th and 20th centuries shows that the greatest danger to the existence of Estonia and Latvia as countries with a West European culture has come, not from Germany, but from Russia. One needs to think only of the russification policy of the late 19th century, and the brutal sovietisation that occurred after 1940. By contrast, the short German occupations in the First and Second World Wars were far less harmful to the Estonians and Latvians.
If the ultimate choice facing Estonia and Latvia was between German and Russian/Soviet rule, then it can be seen that German rule would have been by far the lesser of two evils.
I think my original point still stands. The Estonian and Latvian ruling classes, through their preoccupation with crushing the ethnic German middle class and seeking to turn it into a propertyless marginalised proletariat, and ignoring the birth of Bolshevik power, except to keep it from their borders, effectively cut their own throats. They destroyed any possibility that they would not eventually be overwhelmed by Soviet power and cut off for 50 years from the connection to the West which the German minority had provided for several centuries. Instead of a friendly German minority, they ended up with a sullen, hostile Russian one.
Perhaps the long Soviet domination of Estonia and Latvia represented a sort of poetic justice for the bad leadership of the native middle classes of those countries, driven by ethnic resentment.
But I would think that the descendants of the Baltic Germans are far happier today living in Germany than they would have been if they had stayed in their former homes.