In the course of my 4-year conversion, I had many theological and personal hurdles to jump before coming to full agreement with the Church. Three tough ones (for me) come to mind: intercession of the Saints, adoration of Mary, and Church authority. For most Protestants, the Church's teaching on the Real Presence of Christ in the Eucharist is also a major theological hill to climb, but it wasn't such a big deal for me.
As a Southern Baptist, I had been raised under two very clear principles that would later prove to be catalysts in my conversion:
1) A strong belief in miracles and other "faith-only" principles (in other words, those truths we cannot empirically verify)
2) A motif for interpreting Scripture according to a literal sense interpretation whenever possible
A few months into our 9 month stint in south Florida, my wife attended a Lutheran church. When communion began, the pastor asked her if she believed the elements to be the true body and blood of Christ. Thinking back to the Last Supper, she realized in one quick moment of clarity that she would be silly to not take Christ's words literally. While I did not fully appreciate it at the time, this event would become the primary motivation for moving forward for my wife, and ultimately for myself as well.
I'm not being coy when I say that I've never heard a good argument against Transubstantiation: that is, the doctrine that Christ is really and fully present in the elements of the Eucharist. A protestant can draw arguments from 2 different vantage points: 1) Scripture or 2) Empiricism.
The argument from Scripture is, simply, that the passages in question should be interpreted figuratively. In which case, the Catholic can argue that the passages should be interpreted literally. It's your interpretation vs. mine which turns quickly into a meaningless argument. Forgetting that the Church Fathers almost unanimously taught Transubstantiation, and that there is no good textual reason to abandon the literal sense interpretation, many Protestants are happy to wield a hollow defense of what is, clearly, a political stance and not a theological one.
The second argument is, ironically, more personally compelling and more absurd than the first. This is the argument that the elements can not be body and blood because they are clearly just bread and wine. If it looks like bread, and tastes like bread, then it must be bread. This is personally compelling because I, like my peers, was raised in a modernist culture that values empirical evidence. This is stoutly absurd because a Christian (Protestant or otherwise) has already submitted to some bizarre claims that are outside the realm of empirical verification. I would have a hard time looking a Catholic in the eye and stating that, while I affirm the resurrection, the Virgin birth, Jonah and the whale, the flood, and Genesis' account of Creation, I cannot affirm the words of Christ that those elements are His Body and Blood.
St. Ambrose said it nicely: "Could not Christ's word, which can make from nothing what did not exist, change existing things into what they were not before? It is no less a feat to give things their original nature than to change their nature."
I find the teaching to be a refreshing bulwark against modernism, an exercise of faith. It is also one more way in which the Church makes tactile the intangible. Transubstantiation represents a strange challenge to our faith; we struggle every day to believe those things that are unseen. How much more difficult to believe that something we see and touch and taste is substantially different than we perceive it?
One final note, and I won't dwell long on it because I don't understand the full implication. Jesus says, as recorded in John 6:53, "Truly, truly, I say to you, unless you eat the flesh of the Son of Man and drink his blood, you have no life in you." Here, Jesus equates life or eternal salvation with the consumption of His Body and Blood. Is a symbolic understanding of the Eucharist an acceptable substitute for the clear teaching of Christianity on this subject? Can I claim to have the life Jesus wishes to give, if I, by my own belief, have never partaken of Christ? I trust that God's grace is greater than any disagreement between Protestants and Catholics, but I will continue to read John 6 with unease.