Susan Boyle is a woman of faith who has been thrust from her familiar surroundings and now struggles with how her simple faith fits into the new and strange life she has been thrust into.
In her new life, she is confronted by new experiences and life views that challenge the neat boxes many with faith tend to put God into; boxes that get blown apart when the world around them changes. We find the boxes a comfortable way to fit God into our experiences - and He doesn't necessarily fit in them!
This song is her heart cry to God, asking him to show Himself true and faithful despite all the challenges to her faith that are being thrown at her.
Doubt is scary, and she fears offending God through doubt, but in fact in my opinion, her faith will grow through this - doubt gives God ways to speak to us in ways we can't hear when He is kept in boxes.