Running a Matrix server is complex because the software could be better, not from some inherent user-facing complexity.
Encouraging users to use a VPN can be as simple as bundling the WireGuard installer with your software and providing a list of recommended non-shady VPN providers.
This makes things less complicated for the user, because they benefit from having a VPN whether they use your software or not (to hide their current IP address from any centralized services they still use), but now they have someone they trust providing a vetted selection of them to choose from. And on top of that it gives a free software developer the opportunity to fund some development through the use of affiliate links.