Guardians of the Galaxy is very soft scifi, basically what we refer to as space opera. Being awesome and fun trumps things like the impossbility of crossing interstellar distances in minutes, you know? That doesn't stop some people from dissecting the film's science.
When Peter Quill, aka Star-Lord, first jets out of the Kyln, a high security prison in space, wearing only a face mask and a coat I knew that there would be people online who would complain. There's a modern desire for things to be 'realistic' that hampers not only story-telling but also enjoyment of those stories - isn't the fact that Star-Lord flying through space is a cool image enough for you? When he was exposed to the vacuum of deep space a second time I began actively dreading the nitpickers. "I liked the movie but it bothered me..." would be how all of these tedious tweets and comments would start.
Let's take this one step at a time. The easiest answer here is that Star-Lord's mask, while covering his face, may actually utilize a force field that encases his whole body, protecting him from exposure to space for short durations. That's sort of the No-Prize answer, the one where we fill in the gaps for the creators using ideas that aren't presented in the comic/movie. It would have been easy for James Gunn to show Star-Lord encased in a rippling force field if this was the answer he wanted.
The other answer comes from science, and it's actually better than the force field: yes, Peter Quill, (mostly) Terran, could survive in the vacuum of space without protection for the short amounts of time we see in the film.
This requires one assumption, which is that his mask supplies him with oxygen. I think we can safely assume that, since he bothers to put the mask on Gamora when she's floating unconscious outside of Knowhere. If he's getting air from the mask his brief flight from the Kyln is absolutely within the realm of scientific reason. And when he takes off the mask he mostly reacts as you would if you were exposed to space.
Nobody's quite sure how long you can survive in space, but it's at least one minute. We know this from horrible tests on dogs as well as horrible accidents that have exposed space industry workers to vacuum. You'll only be conscious for about 15 seconds of that minute, though - if you're not getting oxygen you'll be knocked out pretty quickly. And holding your breath won't help; in fact it'll probably kill you, as the vacuum of space would cause your air-filled lungs to swell up and rupture, sending air bubbles into your blood, finishing you off quickly.
There were horrible tests conducted on dogs in 1965 at Texas' Brooks Air Force Base that showed animals exposed to almost complete vacuum for up to 90 seconds survived. It wa a terrible experience for them - they simultaneously shit, vomited and urinated, they swelled up to ungodly dimensions and they had seizures, but after a slow repressurization (and about 15 minutes to shake it off) they were walkng again. They seemed to go blind for a short time, though.
But what about the cold when Quill is flying outside of The Kyln? He's not even wearing gloves! Well, the good news is that while he might have really felt that negative 200 degrees Fahrenheit (unless he was getting direct star exposure, which could mean he was experiencing heat up to 200 degrees Fahrenheit), vacuum is a good insulator. It takes a long time for your body heat to seep out in a vacuum, so you probably wouldn't get frostbite or anything like that, especially if the exposure is fairly quick. As it was there.
Of course he's fully exposed at Knowhere, without oxygen or anything. He does quickly pass out (don't try mapping real world time to movie time. It's subjective), but wouldn't he burst? Everybody who saw the original Total Recall knows you burst.
You don't. You swell - and Quill is getting swollen there - but you wouldn't pop. Your eyes wouldn't even pop out. Your skin, being an excellent seal, would hold you together quite nicely. Your mouth and eyes and nose would cool FAST, and uncomfortably, but you'd be okay. There's a story of a NASA technician who accidentally depressurized his suit in a test chamber in the 60s; he claimed that before he passed out (14 seconds in) he could feel the moisture on his tongue boiling away. This could be why Quill keeps his mouth shut (also probably because the scene looks to have been shot in a pool). The key, of course, is that the exposure is short. If Quill was hanging out in space for two or three minutes we might be having a very different conversation.
The most unrealistic aspect of all of this is that Quill would have woken up in the Ravagers airlock with his body looking like he'd been covered in hickeys, all mottled and ugly, but he'd likely be perfectly fine. He might even be perfectly alert immediately upon repressurization - tests on chimps showed they could go for over three minutes at nearly total vacuum and suffer no cognitive effects.
So yes, Star-Lord could have been out in space unprotected. When it comes to the science behind a sentient tree you're on your own, nitpicker.