Let's oversimplify the algo and just talk about backlink ranking power in very basic terms.
You have a site and it has link ranking power of 100. Things are going great with rankings. You weren't careful in building the link power and took some shortcuts. Unfortunately Google rolls out the Penguin update and now they rule that 50 of your links are garbage. Your link score is 50 good & 50 bad. You know you need to do something to fix the site so you go through and delete suspicious links. Unfortunately you misidentified some good links and deleted them and you missed some bad links. So you now have 40 good and 10 bad. Since you feel like you cleaned up the bad links you sit back and wait for Google to release a Penguin update. Even if Google forgives your site, your link power is less than half power and half power is not strong enough to rank in the serps.
Instead of waiting for Google to release a Penguin update, you probably want to get active and build up positive links that will drive legit converting traffic. It isn't easy and yes it is a huge pain to do this but building up traffic generating links will make you less dependent on Google and at the same time make yourself more likely to rank higher in Google.
I am not saying this applies to all webmasters. I'm more calling attention that you should make sure you have strong enough backlinks to fight for your rankings