All the cafe can see is your connection to a Tor node. Continuing on this, if you want your connection to a Tor node to be anonymous, use a bridge. They are specifically meant to make it more difficult for anyone watching your internet traffic to determine that you are using Tor.

If you want to be completely sure that your connection type/target cannot be identified, you need to hide your connection on the physical layer. A VPN could do this. They create a virtual interface through which your traffic goes before leaving your device. However, using Tor on a VPN connection is a topic of debate, so read up on it, perhaps here(YouTube link!) and here(official Tor wiki), and make up your own mind.

You could also MacGyver a portable Tor router which you physically connect to, either through an Ethernet port or WiFi on your computer and then connect that Tor router to the café's WiFi.

Also, and after this I'll shut up, since you mentioned Qubes: you could also setup a qube to be a virtual Tor router, through which you route your traffic/browsing/surfing from your "working" qube. This, however, requires enabling at least ipv4 forwarding in the kernel and configuring your firewall to enable network address translation.