Because the risk isn't equal. While condoms don't protect from all STDs, when used correctly they protect from many STDs (including AIDS, so long as they're not using dirty needles - but that's typically discussed in sex ed) as well as pregnancy.
Telling teens to simply not have sex because "condoms are useless" would lead to kids having sex without condoms > higher rate of pregnancies and STD spread.
The point isn't to prevent teens from having sex, because that never, ever works in the history of humanity. The point is damage reduction by teaching safe sex so if they're going to do it, which they are, they at least be as safe as possible.