Why do Catholics believe transubstantiated host may still affect the gluten sensitive? I was reading about the Eucharist the other day and read that sometimes in Catholic mass, there is low-gluten bread available for those who are gluten free. The same text said that the bread, once consecrated, ceases to be bread and becomes the body of Christ.

If the bread is no longer bread and indeed the body of Christ, wouldn't it no longer be dangerous to gluten-free people, and if it's no longer dangerous/bread, why cater to the faithful gluten-free? Shouldn't they understand it is no longer bread and instead the body of Christ?

Do I have some sort of misunderstanding of what Catholicism teaches of the Eucharist? I brought this up to my girlfriend who is Catholic, and she said (my interpretation of what she said) that the bread still has its materialistic properties although it has turned into the body of Christ. This didn't really make sense to me at all and I didn't press the issue any further as I felt kind of silly for bringing it up and my lack of knowledge on the subject. Do I have some sort of misunderstanding here or am I looking too deeply into something so "minor"?
Your girlfriend sounds correct. It may sound silly at first, but the doctrine of Transubstantiation is a well developed, detailed explanation of what happens during the consecration of the bread and wine. It is not a minor thing.

The Catholic doctrine of Transubstantiation  teaches that the substance of the bread, what the bread really is, becomes the Body of Christ. The accidents of the bread, the characteristics like color, taste, etc, are not changed. These are properties that are not essential to what bread is. Red bread would still be bread. The accidents include everything that you could determine using chemistry.

The human body will still react to the host because the chemical accident/characteristic of containing gluten remains true.

Gluten-free hosts

Several people have commented/suggested edits about gluten-free hosts. It is my understanding that these are not valid for the Eucharist. See this letter  of then Joseph Cardinal Ratzinger (later Pope Benedict XVI)

To answer a comment:

Note that the words essence , substance , and accidents have a specific philosophical meaning with a history and development that stretches back thousands of years. They don't necessarily agree with how we use the words today, especially if one is coming from a modern, rationalist-materialist worldview. 

It is tempting to say that the chemistry of the bread or its components is the essence of the bread, but that does not coincide with how the Catholic Church uses the term essence. An overview of that would be a good question to post (if it has not already been asked).