Its fine. Cydia's servers are getting hammered. Just let it go and if you get a pop up saying things were not downloaded, go into your Changes tab and click Refresh at the top. Keep doing that until you don't get anymore errors.
I had to do this on 2 devices and it took a couple hours.
Yeah, give it some time. It took several tries for me before it finally worked. And these Cydia apps/tweaks and stuff all have resume downloading. So even though it takes several attempts to download one thing, it still picks up where it left off.