Nature, it is said, abhors a vacuum, and churches abhor ordinary practices that can't be justified in ways that theological standards are. I sigh when certain Unitarian Universalist ministers (whom I otherwise admire) make outlandish claims about the symbolic -- I've even heard the word sacramental -- importance of taking the Sunday offering. Does this mean direct deposit would be a liturgical reform? A crisis of faith?
I bring this up because of the plain division in communion practices seen in Protestant churches. I've only served (and now attend) churches that use small glasses in trays, derisively (if descriptively) called "shot glasses" by the uninformed or dismissive.
I don't particularly like them. They're messy, hard to handle, and noisy. If new, they're expensive or cheaply made. In small churches, they're overkill. (Though I've seen versions that work for very small churches which appeal to the gadget-freak in me. In particular, I've seen a rectangular tray with cut-outs for, say, twelve small glasses with a handle that reaches lenghtwise over the top. Imagine if a traditional milkman was doubling as a parson. The ones I've seen hearken back to hobbiest woodshops, and I love them the more for it. A smaller version of the one on the left of this image.)
While associated with Protestantism, it isn't a particularly old use. Look to all that antique communion silver auctioned out of New England Unitarian churches: you find common cups. The common cup is a livelier symbol of the Great Thanksgiving, a more precious emblem for the church, and heck of a lot easier to carry and keep clean. It is -- as they say in the software world -- a scalable solution. (A flagon helps; indeed, certain Unitarian rites carry over an almost medieval importance to the pouring that I appreciate. Why some Episcopalians make such a deal of the fraction but do nothing with the pouring is beyond me.)
But the reason for the small cups being introduced continues to haunt churches: the fear of contagen. While it may take some convincing, and some basic hygenic steps, the common cup is safe. You probably are at more risk of catching some illnesses by shaking hands or breathing the same air. Receiving an HIV infection isn't in the cards. (Cholera was probably the disease that first prompted the individual cups.)
While there should be extra precautions for immune-suppressed individuals and for communion in a hospital setting, there's no reason to paint the common cup with unfounded charges.
Here's a good briefing paper.
Eucharistic practice and the risk of infection (Anglican Church of Canada)