The team that wins the toss can choose to Receive, Kick, or defer to the 2nd half.
If the team elects to Receive the other team can choose which endzone to defend (Often times based on the wind direction).
If the team defers, then the other team can choose to kick or receive or endzone to defend, (usually will receive because then they may have to Kick-Off both halves).
It's rare but there are times when a team defers to the second half and then they will pick which endzone to defend because of the wind or because of what you are suggesting with the student section and noise.
In the Pitt game, I believe they wanted to defer (so they would Kick-Off) but their captain said they wanted to Kick. Wrong Choice because now they would have to kick-off both halves. (If I remember correctly).
Which someone posted before the video of the Pitt-PSU game when Millen and Clark were captains in street clothes and the Pitt captain couldn't figure out which to choose.
Coaches always have a meeting with the captains after the pre-game warm-ups to discuss the coin toss. They usually designate the one captain that understands the decisions (if this ....than that) stuff and tells the other to keep their mouths shut.
Tongue tied and twisted, just an earth bound misfit, I