It almost seems the main line on chess.com, 3.Bd3 against the Pirc.

Whenever I play the Pirc (well actually I don't intend to play main line Pirc's, I either transpose to the Philidor or I play the Czech System) I see this move a lot here on chess.com.
Is there a reason for this? Is there a video here that recommend 3.Bd3? Is there some popular repertoire book that recommends 3.Bd3?

More importantly I find it irritating (maybe that is the reason they play it), so what is a good way to play against it?

I just took a look at a database since I'd never seen 3. Bd3 in the Pirc Defense. It seems that the usual 3. Nc3 of the Pirc blocks the c-pawn, and in the variations where White plays Bd3 he also plays c3 and Nbd2. Therefore the idea of Bd3 is evidently to protect White's e4-pawn without blocking the c-pawn via Nc3 since White intends to play c3 and Nbd2.

In general, such insights can be derived from a database by exploring similar lines and noting cause-and-effect.

 I really don't know when 3.Bd3 become popular, but it helps Black push e5 which is the objective goal of the pirc player. After 3...e5 Black is doing well.  

I think Bishop_g5 is right: I took a look at a few Pirc games where Black won, in both the usual 3. Nc3 variation and in the 3. Bd3 variation. The 3. Nc3 variation is over 10 times more popular than 3. Bd3, so I don't know why 3. Bd3 might be more popular suddenly: maybe some GM recently had a great success with it. As Bishop_g5 mentioned, 3. Bd3 allows Black to get in an early ...e5, which when combined with the thematic ...f5 move found in both variations, gives Black a strong and aggressive kingside pawn structure. This is in contrast to the 3. Nc3 variation, where Black is more on the defensive since White often plays f4, so Black can't get in the equalizing ...e5 very easily.

These differences can be seen clearly in the following games:

()

3. Nc3 variation

Black has difficulty playing ...e5, so his chances lie on the queenside.

()

3. Bd3 variation

Black can easily play ...e5 and wins in the center and on the kingside. 

AlHuwar (2291) vs. Vedmediuc (2437)

Baku AZE 2016 · Robatsch defence, Geller's system (B07) · 0-1

I used to play this to try and transpose into the white side of the KID

 3.Bd3 is recommended by Sam Collins in "A Simple Opening Repertoire for White"