The biblical reference is from Matthew 18, if that helps:
“They said, “Who is the greatest in the holy nation of heaven?” 2 Jesus took a little child and put him among them. 3 He said, “For sure, I tell you, unless you have a change of heart and become like a little child, you will not get into the holy nation of heaven. 4 Whoever is without pride as this little child is the greatest in the holy nation of heaven. 5 Whoever receives a little child because of Me receives Me. 6 But whoever is the reason for one of these little children who believe in Me to fall into sin, it would be better for him to have a large rock put around his neck and to be thrown into the sea.”
Comics I Don't Understand 
The angel is dubious that the suggestion box is taken seriously, undoubtedly due to her experience with them while still alive. She’s been reassured that it is, and told to have great faith in the system.
“The faith of a child” is an expression meaning “pure, unquestioning faith.”
I don’t know that suggestion boxes are really still a thing, but in the past they were a common fixture of offices. They were often treated as placebos, occasionally emptied but otherwise ignored.
At least two ways this can go.
Dilbert and many other cartoonists before and since viewed suggestion boxes as traps, identifying employees who disagree with the status quo under the false promise of confidentiality. Here, it can be The Boss seeking out the prideful and heretical who think they know better than the status quo. It takes the faith of a child to fall for that in the office and, evidently, here.
Another angle is that the Boss NEEDS suggestions, which doesn’t inspire faith. There was a Mr. Boffe cartoon headlined “A Time to Worry”, in an unimpressed angel holds a playing card as the Almighty awkwardly tries to guess what it is, like a kid botching a magic trick.
Bensondonald’s second angle seems right.
It’s interesting to me that monotheistic religions make God all-knowing, all-powerful (etc.). Polytheistic religions (e.g. Greek, Nordic) have gods with less exalted powers and character flaws. One can easily imagine a suggestion box on Olympus — although that might lead us to a more Dilbert interpretation of that suggestion box. Who would want to tell Zeus he’s wrong?
The suggestion box means the “bosses” obviously don’t realistically expect blind faith. If everyone had unwavering faith they’d have no suggestions, so something isn’t right if the people telling you to have blind faith also ask for suggestions. It isn’t a trap or just a feel good ploy, but more a direct conflict of the most basic directive.
I think the statement “something doesn’t seem right” is there to guide the reader to realize the conflict of a suggestion box and saying everyone should have blind faith.