I can’t speak on behalf of any denomination - only myself, and I’m a mutt - my dad is Christian (Desciples of Christ) and my mom is Roman Catholic. Transubstantiation is one of those things of most organized religions that leaves me scratching my head thinking, really?
Personally, I have always seen communion as a symbolic act of sharing in the body and blood of Christ. Not once have I ever thought that I was actually eating flesh and drinking blood. I agree there are many mysteries about God and the nature of faith, but I don’t see this as one of them. Frankly, it’s issues like this (among many others like confession and the infallibility of the Pope) that resulted in me choosing not to go through confirmation. If it’s a choice between “Believe what we say or else…” (the implication ranging from not belonging to the church to risking my immortal soul to eternal damnation), I’ll go my own way.
Not all Catholics believe in transubstantiation. I watched on one of my favorite historians/authors, Garry Wills, on The Colbert Report on 2/11/13 dispute the subject, stating that Augustine (a 3rd century Catholic - granted, but a valid respectable source) said it was ridiculous to say that we eat God, that we digest God, and excrete God. Wills went on to say that Christ, at the last supper said, “Eat this bread, it is my body”, he didn’t say “take a chunk out of my arm or tap my blood”. No wonder Wills won the Pulitzer with such wit and wisdom like that…