I would imagine it means creating a rainbow table for a particular set of prime numbers. From the article it sounds like many applications use a small handful of prime numbers. A DH key exchange uses two prime numbers (shared publicly) and two secrets (kept, secret...).
In theory the NSA could enumerate ginormous rainbow tables for a large set of secret keys.
Perhaps someone else on HN can provide a more detailed description of the suspected attack?
Edit: the responses to smegel's question below seem much mor e thorough and accurate than mine!