politeness - In actual Japanese society, how often are second-person pronouns used?

My Japanese professor (I'm in first-year Japanese) advised us to primarily avoid the use of second-person pronouns like あなた or 君 or おまえ throughout the year, and essentially treated their utterance as something of a faux pas. However, I've been exposed a lot of Japanese language media (primarily anime and music) and their use therein seems to be pretty okay. I understand that あなた is used by wives to refer to "their dear husband" or something, and that 君 and おまえ are ostensibly inappropriate (the latter considerably more so), but do Japanese people in Japan actually pay attention to these distinctions? I'm inclined to think that my professor advised against their use (as well as the use of a slew of other words I attempted to use from my experience, including 俺、彼／彼女 and あいつ／あいつら) simply to avoid beginning our instruction with something overly informal.

tl;dr version: Are second-person pronouns as societally ill-advised as my professor would like to have me think? In what contexts (e.g., with friends, with older family members, with colleagues, or with superiors) are their use acceptable?