Ah yes, OK, I see what you mean.
Arguably the stronger relationships are the AY and AF ones where BE is effectively flying for the other carriers. The BA shareholding came about - as I understand it - as part-consideration for flyBE's acquisition of BA Connect, rather than BA wanting a strategic investment in flyBE as part of its network options.
With this Brussels Airlines deal (like the Olympic one a couple of years ago), BE is essentially providing cost-effective feeder capacity, much like the regional carriers in the US do for their mainline partners. What's interesting is that in the US, it's common for a single regional carrier to fly for two or even three competing mainline carriers, i.e. to have subfleets painted in the different liveries. In parallel with their "own" network, perhaps this is one path forward for flyBE?