Historically, the word "penalty" has been thrown around pretty loosely for sites who suffer in Google rankings. However, just because you got hit by an algorithm update, it doesn't mean you've been penalized, as far as Google is concerned.
Google defines penalty as "A punishment imposed for breaking a law, rule or contract."
So, technically speaking, if you got hit by Penguin (legitimately), you're being penalized for breaking the rules (Google's quality guidelines). That's what Penguin is designed to do. However, Google views penalties as manual action, as opposed to algorithmic action.
Google's Matt Cutts spoke with Danny Sullivan in a keynote discussion at SMX last night. Danny asked if Penguin is a penalty, to which Cutts responded (according to Search Engine Land's liveblog), "We look at it [as] something designed to tackle low-quality content. It started out with Panda, and then we noticed that there was still a lot of spam and Penguin was designed to tackle that. It’s an algorithmic change, but when we use a word like 'penalty,' we’re talking about a manual action taken by the web spam team — it wasn’t that. We don’t think of it as a penalty. We think of it as, 'We have over 200 signals, and this is one of the signals.'"
According to the live blog, Danny asked, "So from now, does 'penalty' mean it’s a human thing?"
To which Cutts responded, "That’s pretty much how we look at it. In fact, we don’t use the word 'penalty' much, we refer to things as a 'manual action.' Part of the reason why we do that breakdown is, how transparent can we be? We do monthly updates where we talk about changes, and in the past year, we’ve been more transparent about times when we take manual action. We send out alerts via Google Webmaster Tools."
Search Engine Land editor Barry Schwartz, who also liveblogged the discussion, writes, "Google's Matt Cutts made it crystal clear last night. If you get those Google Webmaster Tools notifications or messages, that means you have been hit by a manual penalty done by a person at Google after reviewing your site by hand. Got that?"
On a side note, Cutts indicated that only about 1-2% of 700,000 Webmaster Tools warnings were about links, and the rest were clear violations.