3.Nc3 seems preferable because white retains the option of playing f3, or f4.
Modern Defense: Why 3. Nc3 over 3. Nf3?

That's correct. In passing, allowing 3...e5 is not a bad thing at all. 3...e5 4.dxe5 Bxe5 5.Nf3 looks quite good for White after either 5...Bxc3 6.xc3 or 5...Bg7 6.Bc4
OK, thanks everyone, that makes sense, especially now that I looked at the continuation 3...e5 in a database. I was surprised that Black gets such a weak position after that: 3...e5 is actually rare, after that move White wins 80% of the time as of move 3, 100% of the time as of move 6, and on move 7 there were only two games in the database, both wins for White. The following was one game of those two games, the game with the highest rated players. It's very instructive, and I learned some useful things from it, especially the pawn-weakening Bg5 trick when Black is uncastled.

White does not want to commit to pushing his f-pawn or not pushing his f-pawn on move 3. Since the general pawn structure dictates that white should attack on the kingside, white will often push his f-pawn to f4, or more often to f3 to support g2-g4 (and to stop N-f6-g4 ideas if the white dark-squared bishop comes to e3). In some other lines, of course, white wants to play Ng1-f3, but it all depends on which defense black employs--which is why white does not commit with 3.Nc3.

And yes, if black ever plays ...e5, then he only plays it after d6. It's called the "Modern Defense" for a reason: it uses hypermodern strategy, which takes a restrained hand in the center.
Black's numerous plans in this position include c6-b5, d6-e5, or even c7-c5. All attempt to prove that white's center is weak.
Here, 3...e5 just loses a tempo to 5.Nf3 as you rightly pointed out.

It's called the "Modern Defense" for a reason: it uses hypermodern strategy, which takes a restrained hand in the center.
Yes, I missed that connection based on the name: the Modern Defense is like the Vienna Game in that they're both hypermodern and White either outright plans to play f4, or noncommittally reserves the option to play f4.

It's called the "Modern Defense" for a reason: it uses hypermodern strategy, which takes a restrained hand in the center.
Yes, I missed that connection based on the name: the Modern Defense is like the Vienna Game in that they're both hypermodern and White either outright plans to play f4, or noncommittally reserves the option to play f4.
Look for Duncan Suttles games with the Modern.
In the Modern Defense (1. e4 g6 2. d4 Bg7), why is 3. Nc3 twice as popular over 3. Nf3?
It seems to me that 3. Nf3 would be better since it immediately prevents Black from playing 3...e5. I see that 3. Nc3 prevents Black from playing 3...d5, but is it more important to prevent ...d5 over ...e5?
Or is there a different idea involved? The idea could be that White wants to allow f4 since the opening could easily transpose into the Pirc Defense, then that f4 would allow White to play the strong Austrian Attack. However, I looked at the main lines of the Modern Defense, and although some had White playing f4 and eventually transposing into the Pirc Defense, f4 was never the preferred move in any of the lines I saw, and none of the games I saw without f4 transposed into the Pirc Defense, which seemed odd.
1st most popular 4th move for White (4. Be3):
2nd most popular 4th move for White (4. f4):