Absolutely. Depending on how an organization manages its own IT security, data can even be more secure in the cloud than it would be on premises.
Decent providers like Atlassian invest in their IT security and employ dedicated security experts, something that can't be said of all organizations that host their software on premises.
However, I think in some cases being able to run specific software on premises is still a valid concern. Compliance is only one possible reason. Being able to easily access your data outside of the vendor's software might be another.
While they can be addressed, alleviating compliance concerns often is no easy task either, especially if your organization has to comply with laws and regulations from different jurisdictions. For example, I know of one organization where developers are allowed to use most Amazon services but are explicitly forbidden to use Amazon SES because that service currently is only available in a region that's technically outside (EU but not the same member state) of the jurisdiction the organization is in.