The simple present is for 1) routines; 2) schedules; and 3) general truths.
1) In Indonesia, during musim hujan, it often rains in the afternoon.
2) The train leaves at 9:00.
3) Many Indonesians like durian; I do too.
"Today it rains" does not make sense in English except in a very specific and unusual context.
Just because Duolingo accepts an answer does not mean that the response is grammatically correct. You must account for human error (and there are plenty of mistakes as well as errors in these translations). Additionally, Duolingo's software is not yet able to accurately handle the intricacies of some languages--the Norwegian program is rife with English apostrophe errors, for example. What I can assure you, unequivocally, is that, "That's rain" does not mean, "It's raining."
"That's rain" is certainly a correct English sentence, but it means something different than what the translation suggests. That's + (a noun phrase) is used to identify something. That's rain. That's snow. That's sleet. That's hail. Those sentences are very different than these: It's raining. It's snowing. It's sleeting. It's hailing. Each of those sentences shows aspect--that the verbs action is happening at the time, not just habitually.