Because planets actually do twinkle. Most people were told that the major difference between stars and planets is that only the former twinkle - but that's an oversimplification. Given the right conditions, planets will twinkle too, it just happens more rarely.
Several factors that contribute to it:
lots of air turbulence; or, as astronomers call it, "bad seeing"
closeness to horizon; if the planets are high in the sky, the air column is shorter so there's less chance they will twinkle; but when they are low, their light goes through more air and so it is perturbed to a larger degree
The observation you've made, Venus twinkling, is not very unusual. Many stargazers are used to seeing that once in a while. I've seen Venus scintillate several times in the past, always at sunset when it was about to drop below horizon; I would presume you could see the same behavior very early in the morning as Venus has just risen.