Yes. There's flour in dough but other things too (if only water in the simplest of cases, but often yeast -or a sourdough starter - and flavourings). It's wrong to say you knead the flour.
Kneading flour would be a pointless and very long activity. The combination of flour, water, yeast, bicarbonate of soda, baking powder etc is dough. The simplest dough is just flour and water but many doughs contain more ingredients than that.