So the audience could see his dick, that's why. It's quite rare to see a decent full monty shot in a mainstream horror movie.
You've seen Guy Standeven in something because the man was in everything.

So the movie had a nude scene.

Sheets could have been hastily taken for some other purpose.
Clearly, it symbolizes he rebirth as a stranger in a strange land.
I couldn't believe when I read his filmography that he played a toilet (no joke) in According to Jim

My question is how long has he been there? He hasn't got a catheter attached and he hasn't soiled himself so can't be more than half a day right?

It's suppose to represent Jim's rebirth into a new world he isn't familiar with. The Commentary track explains this.
I believe the main question being asked in this thread is what is the practical, real life context for him being naked rather than what it's suppose to symbolize.
Search your feelings, you know it to be true.
u007f
https://goo.gl/fZ0xWS

THIS!^

It's suppose to represent Jim's rebirth into a new world he isn't familiar with. The Commentary track explains this.

Maybe whoever was the last to see him (nurse or Dr) thought it was best that he not have anything on. Maybe they thought he might get tangled in the sheets or maybe as another poster said he was getting a sponge bath. I really don't think it was anything to do with symbolising man and ape or vulnerability Whoever was there was obviously trying to help him as they locked him in so he'd be safe and they left the key.

He came from a nudist colony, he didn't have clothes on to begin with
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Experimenting? Hijacked?
He got knocked off his bike by a car and cracked his head open which put him in a coma.

I thought that too - also the way he had a scar and shaved patch on his head made me think they were attempting to dissect him and experiment on him. I wish we got more information on that. I found it a little odd how he was even in a coma for so long in the first place, how his parents knew about it, how he had been hijacked and knocked out before even discovering the virus existed, etc I guess it's more of a neat way to begin a story than anything else.

I think it was to liken man to the ape in the previous scene (more generally of course), shown in a similar position on the bed. The film has a lot of subtext about how animalistic humans can be. I think it says, "Humans are good enough test subject," or something of the sort.
At the very least I believe it connection human to our "more" animalistic apes in some way.

I think it was done more to drive home the utter vulnerability of the character. What more of a vulnerable situation can you be in than to be naked in a hospital full of infected people who want to tear you apart. Or Perhaps he was in the middle of being sponge bathed when the hospital was overrun.