I think part of it is that the internal use of toothpaste people are skeeved out by someone else touching it or having used the tube. A possible solution? Provide something like a Colgate Wisp--http://www.colgatewisp.com/wisp/HomePage
I seem to recall having rec'd a small toothbrush and about a 3ml tube of toothpaste last time I flew Virgin Atlantic. That's about a toothbrushing worth.
I tweeted about this in May while traveling for work while lamenting the absence of toothpaste in my high scale hotel. I get the skeeved out factor but I'd prefer toothpaste of questionable origins (or just the very small travel size one) to nothing. Also why do they give out lotion and not toothpaste?!?
On theory not posited: as something that goes in your mouth, and that also comes in many different varieties, toothpaste is an individual taste thing in a way that shampoo is not. Lots of people have a favorite shampoo brand/type, but can deal with using whatever the hotel's providing for a couple of days. But if you like gel and the hotel gives you paste (or vice versa), then you're going to need to acquire your own, anyway.
I believe most hotels will bring you a toothbrush and toothpaste if you ask for it. (I have forgotten mine more than once...)