Qu'est-ce que tu en penses? -- What do you think of it?
Qu'est-ce que tu penses? -- What do you think?

It depends on what you want to say.

instead of "Qu'est-ce que tu penses ?" 

Qu'est-ce que tu en penses? -- What do you think of it?

What do you mean by "why do we say this"?

I am surprised at this. As a native English speaker I would say that "What do you think?" means the same as "What to you think of/about it?" You can drop the "of/about it" when the context is obvious. I'm obviously not a native French speaker, but I would have thought you can't do the same thing in French, so "Qu'est-ce que tu penses?" is either wrong, or implies a direct object, so it would have to mean something like "What are you planning?".

Maybe "What are you thinking." is the better translation, in the sense of "a penny for your thoughts" :)

But is that how you would say it in French? Wouldn't it be "À quoi tu penses?"

According to a French native speaker, both is possible:

Qu'est-ce que tu pense. -- What are you thinking about?
À quoi tu penses. -- What are you thinking about?

According to her, they are both possible and mean exactly the same thing: asking someone what he is thinking, without reference to anything mentioned earlier.

Qu'est-ce que tu penses, of course, I forgot the "s". Wish there was some way to edit one's typos...