Your sentence should read
They are always among the trees and the flowers.
It is idiomatic. For example, to say
I ran through trees in the forest.
would be understood to mean you knocked down a bunch of trees, whereas
I ran through the trees in the forest.
means you ran among the trees.
In the same way
They were dancing among the flowers.
She was picking flowers and counting the petals.
Both of your sentences
They are always among trees and flowers.
They are always among the trees and flowers.
are understandable and mean the same.
"The" refers to the specific group one has in mind, "We brought the presents for our friends" is a specific group of presents. "The trees" in this case would be interpreted as the trees near the birds, where they are flying around since they wouldn't be in trees on the other side of the world. "The trees, the birds, and the flowers of Yosemite make it unique" since they are specific groups to Yosemite.
The use of "the" is not necessary, but is nuanced to a native speaker.
This is different to "We ran into opposition" means someone conceptually opposed you about something versus "We ran into the opposition" which means you physically ran into the people who oppose you.