The Apache Software Foundation is a non-profit foundation. It has no owners, similar to how natural persons have no owners.
Instead, the foundation is controlled by a board that is elected by the foundation's members. A company could effectively take over a foundation by getting its employees elected into the board, but they would have to convince the members first – not particularly likely for such a lively foundation. Thus, fears about an imminent takeover are unfounded.
Various companies sponsor the Apache foundation. For example, Atlassian contributes licenses for its Jira and Confluence products. Apache and Atlassian have something to do with each other in the sense that they use each other's software.
Apache software is generally offered under the permissive Apache 2.0 license, which allows commercial use and reselling. If Atlassian offers its own products based on Kafka or Apache HTTPD, they are totally allowed to do that, just like anyone else.
The Apache Kafka project is currently led by Jun Rao, who originally developed Kafka at LinkedIn and co-founded Confluent (not Confluence!). Confluent was founded by Kafka developers. This is not a case of corporate takeover of an open source project. This is more like the ideal open source story: that some developers build awesome open source software and are able to finance themselves by working on this software. For example, Confluent offers Kafka training and adds value-add software on top of Kafka. While close cooperation between a company and a foundation's open source project would raise eyebrows e.g. at GNU, it is perfectly normal in the more enterprise-friendly open source world around the Apache, Eclipse, or Linux foundations.