Pro Football Focus does keep track of which defender was covering each receiver, but only on the plays where that receiver was targeted. If you're a paid subscriber, you can see that info by going to the individual game and then to the "Receiving" or "Coverage" tab.
For instance, in the Super Bowl Hakeem Nicks was targeted 13 times, with 10 receptions for 110 yards, 37 YAC, and a long of 19 (and no TD, INT, or dropped passes). 5 of those targets came with CB Devin McCourty in coverage, resulting in 5 receptions, 60 yards, 20 YAC, and a long of 19. 4 targets came against CB Antwaun Molden, with 4 receptions for 45 yards, 16 YAC, and a long of 18. 3 targets came against S Patrick Chung; all 3 fell incomplete. And 1 came against LB Rob Ninkovich, which was caught for 5 yards.
If you're trying to play matchups to decide which WR to start, you could also check out
Football Outsiders, which keeps track of how well each defense has done against each type of receiver (WR1, WR2, other WR, TE, and RB). That includes the yards per game allowed, the passing attempts per game, and also the offensive efficiency on those plays (using their stat, DVOA).