What ancient scripts ultimately capture is part or whole of a tongue spoken in antiquity. However, as you may have noticed, all human languages evolve over time. For instance, English poems written in Shakespeare's time don't rhyme correctly anymore, but a look at their archaic spelling indicates that they should rhyme.
As changes accrue over time, ancient texts become unintelligible if the knowledge of the language is lost. In some cases, the texts can be read, but cannot be understood. The best example of this is Etruscan, which is written in a script nearly identical to the Roman alphabet, so individual sounds and words can be isolated. However, since nobody knows what the words' meanings and the grammatical rules of Etruscan, the texts remain relatively obscure.
Alas, not all is lost. If ancient language had survived and evolved into later, "daughter", languages that can be understood, then it becomes possible to know something the "parent" language as well as the processes involved in the evolution. This study of language change through time is called historical linguistics.