Our D3 team showers together, both men and women (not together, just both teams do it). Some kids choose not to and those of us that shower together definitely think it's weird that they don't, but no one is given a hard time for it. Also not everyone is in the shower at the same time because we have different workouts that take different time, more so in track than in XC.
We also play music really loudly and occasionally we turn off all of the lights and scare the fvck out of each other. But you have to be sure that you aren't touching someone's dick. It's also weird to look at someone's dick, if you need for your own curiosity make sure they are looking away. It's really not that interesting, I would recommend just not looking.
Other shenanigans include fake boxing each other, everyone giving a weird stare to a person who drops the soap, dancing so your junk swings around and messing around with one of those skinny rods that you mark your driveway with in the snow.
It was a little weird for me the first few days but after that it was normal. Whatever you do, as a freshman, don't make it weird, if you choose not to shower with the team then don't mention it. They know you feel uncomfortable. I would say no matter how weird it feels showering naked, just do it, and if after a week it still feels uncomfortable, the stop.
Also, if you have guys with lots of different mileages, like my team, some guys may run 5 miles while other guys run 9 miles. So you usually end up showering with who you run with. Almost all of the freshman that come into our program ran low mileage in high school and our coach usually has them get up to 45-50 and they all end up doing pretty much every run/workout together, so most freshman are in the shower at the same time.
You will be fine. Showering is the least of your worries as a college freshman.