I seriously doubt that rainwater *as it falls from the sky* is more contaminated than well or municipal water.
However, what happens to it after it hits your roof is a significant concern. You get your biological contamination -- bird poo, parasites, fecal bacteria, etc plus all the microbiological fun that they support when the water is stored in a barrel or cistern -- and also your chemical contamination from whatever the roof and gutters are made of. AFAIK asphalt shingle, tarpaper, and cedar shake roofs are considered Not Good, galvanized is considered questionable, painted metal is considered questionable by some but prolly not a big issue for animals only, and tile roofs are considered the safest.
Personally I don't think I'd use stored collected water for animals unless I really really *had* to. If I had a tip-bucket or other system to discard the early part of the runoff I might use roof water to fill troughs directly after a rain, I suppose, if I had a painted metal roof (I actually do think about doing this, sometimes, from my horse shed roof).
I don't see as much problem with funnelling it into a duckpond (which is presumably exposed to many of the same sources of bacterial/viral contamination anyhow). Dunno as I'd put shingle or tarpaper runoff into a tiny in-ground pond that couldn't be dumped and would concentrate toxins, but if it's larger, or if it's something that is dumped and refilled periodically, I don't think you'd have too many worries about Stuff building up.
Storage is tougher, though. Especially with modern attitudes towards what constitutes an acceptible level of cistern-caused disease. If you
really wanted to store it for animals, I'd think yeah you probably should have
both a tip-bucket type system (to discard the early part of the runoff, which will carry more crud from the roof) AND a purification system. Ideally the purification system should include not just a filter (a large drip-type sand canister would probably work, you'd just have to give it time to drip since you'd have little water pressure) but ALSO a u/v unit to kill bacteria and viruses too small for the filter to catch. Unfortunately I think it might be not only expensive but *difficult* to run a u/v unit on an unpressurized intermittantly-used water line. (The bulbs are expensive, they mustn't be run when the line is dry, etc). Without the u/v unit, you're basically taking chances with dysentery and disease for the animals. Most likely you'd get away with it *most* of the time, it just depends how you feel about problems that occurred.
Here is a very useful link:
http://www.harvesth2o.com/resources.shtml
JMO,
Pat