During the one year when I had to share a bedroom, in bunk beds, with a roommate, I jerked off every night that I didn't fuck. Most of the time I'd finish before he came into the bedroom. Sometimes, I'd hear him coming from his desk in the study over to the bedroom and I'd stop until he had gotten into bed (he was in the top bunk). He may have known what I was doing when he came to bed on those occasions, but he didn't say anything, acting as if I were asleep, as I was acting asleep. After he got into his bunk, I wouldn't even wait a minute before jerking again. The thing is, though, that being uncut I don't make much noise or disturbance jerking off - I just pull the waistband on my boxerbriefs under my balls, hold the sheets up like a tent with one hand and jerk off with the other. Even then, jerking off my uncut cock, I mostly just massage my foreskin over my cockhead. Sometimes it would make a "pop pop" sound, but usually it wouldn't be loud enough to be heard over the white noise from outside traffic. Growing up in a house with very thin walls, I've mastered the quiet cum.
One night I awoke to find my roommate jerking off - the upper frame of the bunk bed was shaking a bit and I heard some smacks, but that only happened once, so he was either really quiet the other times or only did it that once. He didn't groan when he came. I know he's cut from, well, the unbuttoned fly of his boxers on a few occasions and a badly performed rugby tackle, so maybe the noise from jerking off depends on circumcision status.
My advice is to jerk off, but try to be discreet. He'll probably know you're jerking off, but will appreciate the discretion if he has a moral problem with it. If he's open about it, well, he might talk to you about it, like my second roommate would.