Rammus is far too well protected with his armored shell to get defeated by Rek'Sai in an actual fight, yet at the same time Rammus doesn't have the offensive adaptations to deal with Rek'Sai's similarly well protected body.
In addition, Rammus' ability to create tremors in the ground likely has an adverse affect on Rek'Sai's tremor sense. When Rammus travels through Shurima, Rek'Sai likely can't get anywhere near Rammus because her only chance to defeat Rammus is by ambushing him through her tunnels, but if she can't detect Rammus' exact location through her tunnels she really can't get the jump on the Armordillo.
It's likely a case of Rek'Sai lets Rammus do his thing because she can't really stop him from doing his thing.