When they are operating their business within the EU, yes. For example US companies operating servers in the EU must comply with EU data protection laws regarding information on those servers. This situation is analogous. WhatsApp's servers are in the US so US law applies. If the servers were in the EU then EU law would apply, not Brazilian law.
More accurately, US companies processing personal data of EU citizens must comply with EU data protection laws. It just so happens that locating the servers in the EU is among the easiest ways to comply with that.
The Brazilian case isn't about data transmission though. WhatsApp isn't in breach of any rules about that. It's about court ordered access to records stored on an server in a specific geographic location - The USA. Now if the Brazilian government passed a law requiring WhatsApp to record all data on servers in Brazil that would at least be possible to comply with.
Whatsapp can choose to assign resources to this issue, or it can ignore it and let it solve itself. If Whatsapp thinks that Brazil is an interesting market for whatever it is selling (what are they selling?) or if it is good for PR then they may choose to seek ways to intervene.