How do the lyrics actually correlate to Rin's situation? Let's take the chorus, one verse at a time:
And it's a long way forwardnote Where to? You're drifting in deep space without the slightest hope of reaching a potentially habitable planet before age will get to you, so trust in menote Who? Rin or her father? And why? What are you hoping to achieve?
I'll give themnote Who? The people of Earth are all dead. shelter like you've done for me
And I know I'm not alone; you'll be watching over usnote Who will be watching over who? The ship's AI is the only one watching and Rin is the only one being watched over. There's nobody else left - they're all dead.
Until you're gone...note Does it really matter now?
It's actually quite scary and haunting (and sad, too) to think about Rin being perhaps the last surviving representative of humanity, floating aimlessly through space, alone in virtual world..., which makes Shelter's ending more inclined to a Bad Ending in overall.
Many of Rin's problems could have been avoided if Shigeru had included the ability for Rin to create a friend to keep her company inside the virtual world. Perhaps a dog, another person, or even an avatar that looks and acts like him. Rin may have never seen a dog and thus is unable to create one, but you'd think there'd be some option, and the ending could have retained its bittersweetness if Rin realized none of her friends in the simulation are real but still saw her father's real memories and realized she's not truly alone.
