The difference between the two sentences is that Dobrý den. means Good day. and you say it when you greet someone. If you say Hezký den!, you wish them a nice day (or Hezký víkend! - a nice weekend). You can say Hezký víkend! on Friday for example, but then when you meet someone on Saturday, you'll not greet them with Dobrý víkend., instead, you'll again say Dobrý den. (both on Saturday and Sunday).
I just would like to add one little thing here, normally you wouldn't say Dobrý víkend to any one, it sounds awkward. The only chance I can imagine to say "dobrý víkend" is, when you are talking with friends about your weekend on Monday and you say it was a good weekend: Byl to dobrý víkend.
Of course, it is essentially the same word, just pronounced and spelled slightly differently :-) The literal translation of weekend, would be "konec týdne", which literally means "(the) end of (the) week". But that's two words and nobody ain't got the time to say that on Friday afternoon!
I wonder what people called it say 200 years ago, aside from the fact that a lot of Czechs actually spoke German as the first language back then, I doubt they said "víkend". Then again, weekend as two days of not working is a rather modern luxury so maybe they did not really need a word for that as Sunday was the only day people did not work.