What was meant by Groot saying 'We are Groot'?

Groot is a hyper-intelligent, tree-like organism from the species Flora colossus native to the planet X. While he possesses human level intellect, Groot's robust and heavyweight physiology causes the organs of his acoustic generation to become stiff and inflexible, rendering the limits of his speech to the simple phrase, "I am Groot."

Source: Marvel Cinematic Universe Wikia > Groot > Biography > Early Life > Criminal Record (1st Paragraph)

up until then all Groot could really say was those 3 words however in the scene in question we see Groot strain to say "We".

why? same reason why he protected them knowing he would die which is reflected by Drax earlier on

Drax: I want you all to know that I am grateful for your acceptance after my blunders. It is pleasing to once again have friends. You, Quill, are my friend.
Peter Quill: Thanks.
Drax: This dumb tree, he is my friend.
Groot: Mmm.
Drax: And this green whore, she, too...
Gamora: Oh, you must stop! [Nebula intercepts their progress across the Dark Astor]
Nebula: Gamora, look at what you have done. You have always been weak. You stupid, traitorous... [suddenly Drax a fires a shot at Nebula sending her flying off]
Drax: Nobody talks to my friends like that.

Source: Transcripts Wikia > Guardians of the Galaxy

at the start of the film the 4 groups of them (Quill, Gamora, Drax and Rocket and Groot) were more or less alone (well Quill have the Ravagers) and infact Rocket's only friend was Groot and vice versa. they also have some social problems as shown at Knowhere

Rocket: He thinks I'm some stupid thing! He does! Well, I didn't ask to get made! I didn't ask to be torn apart, and put back together, over and over and turned into some...some little monster!
Peter Quill: Rocket, no one's calling you a monster.
Rocket: He called me vermin! She called me rodent! Let's see if you can laugh after five or six good shots to your frickin' face! [as Rocket points his weapon at Drax again Peter stands in front of him]
Peter Quill: No, no, no, no! Four billion units! Rocket! Come on, man. Hey! Suck it up for one more lousy night and you're rich. [Rocket hesitates for a moment then lowers his weapon]
Rocket: Fine. But I can't promise when all this is over I'm not gonna kill every last one of you jerks.
Peter Quill: See? That's exactly why none of you have any friends! Five seconds after you meet somebody, you're already trying to kill them!

but by the end of the film they have grown closer together and in the second film they see one another as a family (which is one of the main themes to the second film). with the Dark Aster falling their deaths guaranteed unless something saves them. so Groot did the selfless thing and knowing he would die, shield Rocket and his new friends

[Rocket crashes the Milano into the bridge and seemingly destroys Ronan, the group then huddles together as the ship starts to plummet, Groot forms a giant nest around the group to keep them shielded]
Rocket: No, groot! You can't, you'll die. Why are you doing this? Why?
Groot: We are Groot. [the ship then crashes] [everyone in the group has survived the crash except Groot, who is now a pile of twigs strewn all about, Rocket holds a bunch of the twigs in his hand in sadness]

now while Rocket is able to tell the difference between the various "I am Groot" it's possible that "We are Groot" had some other meaning but given that he strained to say "We" so it's quite possible that he actually did mean to say "We are Groot" in a literal way.

the meaning behind it if we take it literaly can be seen in Rocket's previous comment that Groot would die so "We are Groot" could be Groot expressing that he'll live on though his new friends. Groot isn't just a big dumb tree, he's a big dumb tree with 4 friends and those friends mean a lot to him