David wasn't learning to speak the Engineer's language, he was learning ancient languages in order to be able to decode the Engineer's language. This is based on the theory that human languages are derived from the Engineer's language.
In the scene David is learning the building blocks of language and we see him taking a lesson in Proto-Indo-European (PIE) Linguistics, where a holographic professor, takes him through the ABC’s and recites Schleicher’s Fable. An artificial text composed in the reconstructed PIE, in 1868, to demonstrate the language’s use.
- The linguistics of Prometheus – What David says to the Engineer