I was always under the impression that to patch the free version of ESXi you needed to download the patches, and transfer them to a VMFS volume, then patch that bundle. A great blog VMware Front Experience posted an article about manually patching your ESXi 5.5 host which is just fantastic.
They have also posted a blog about how to patch the latest 5.5u1 bundle.
# open firewall for outgoing http requests: esxcli network firewall ruleset set -e true -r httpClient # Install the ESXi-5.5.0-20140604001-standard Imageprofile from the VMware Online depot esxcli software profile update -d https://hostupdate.vmware.com/software/VUM/PRODUCTION/main/vmw-depot-index.xml -p ESXi-5.5.0-20140604001-standard # Reboot your host reboot
This command can be modified for any new bundles, the KB lists the package name.
When you go to run this set of commands on a system, it will sit there for several minutes. Keep in mind the patch bundle is 300+MB, downloading it, installing it, etc. This all takes time. Especially on a slower internet connection. Using this command recently, on newly deployed VM hosts, saved several reboots (and much time) later on.