I don't have a tag for these, but a couple fics do come to mind. Some of these contain Sam getting hurt in other ways than on a hunt, but I thought I'd include them anyway just in case:
Sufferance (http://utsusemia.livejournal.com/41462.html) by utusemia: "Eighteen months, two weeks and four days. AU from 5.04-that phone call was the last time Sam and Dean talked, but Dean never saw the future." (Gen; Dean isn't present at the hunt where Sam gets hurt, but other than that it fits your request)
The World Devours Me (http://varkelton.livejournal.com/45647.html) by varkelton: "Dean thought he was doing the right thing when he let Sam walk away from hunting.....away from him. Sam thought the separation was nothing more than he deserved. They both thought Castiel had found a way to keep Lucifer from finding them. Neither one of them knew how wrong they really were." (Sam/Dean; this is Sam hiding how much Lucifer's hurting him in season 4, and it gets really dark so heed the warnings)
Cold Streets, Warm Sheets (http://archiveofourown.org/works/732828/chapters/1361940) by seeemrunning: "Sam Winchester is thirteen when the motel manager comes knocking, and sixteen when his job gets him into trouble." (Gen; Sam attracts the attention of a pedophile, and John is a neglectful asshole; first in an ongoing series)
Worth It (http://archiveofourown.org/works/664521/chapters/1212920) by alex_l_kerr: "Tag to Plucky Pennywhistle's. When they get back to the motel room, Dean discovers Sam's been hiding his injuries." (Gen)
no subject
Sufferance (http://utsusemia.livejournal.com/41462.html) by utusemia: "Eighteen months, two weeks and four days. AU from 5.04-that phone call was the last time Sam and Dean talked, but Dean never saw the future." (Gen; Dean isn't present at the hunt where Sam gets hurt, but other than that it fits your request)
The World Devours Me (http://varkelton.livejournal.com/45647.html) by varkelton: "Dean thought he was doing the right thing when he let Sam walk away from hunting.....away from him. Sam thought the separation was nothing more than he deserved. They both thought Castiel had found a way to keep Lucifer from finding them. Neither one of them knew how wrong they really were." (Sam/Dean; this is Sam hiding how much Lucifer's hurting him in season 4, and it gets really dark so heed the warnings)
Cold Streets, Warm Sheets (http://archiveofourown.org/works/732828/chapters/1361940) by seeemrunning: "Sam Winchester is thirteen when the motel manager comes knocking, and sixteen when his job gets him into trouble." (Gen; Sam attracts the attention of a pedophile, and John is a neglectful asshole; first in an ongoing series)
Worth It (http://archiveofourown.org/works/664521/chapters/1212920) by alex_l_kerr: "Tag to Plucky Pennywhistle's. When they get back to the motel room, Dean discovers Sam's been hiding his injuries." (Gen)