(Found here.)
As you can see, the ray-finned fish evolved from the paleoniscoids, while tetrapods evolved from the crossopterygian fish. The tetrapodian line of descent did not go through the ray-finned fish.
I must have missed your source for TLR4-mediated endotoxin recognition and signaling in Fish (though I admit that you can point to most/all other TLR functions)...
TLR4 is present in most ray-finned fish but may be absent from the pufferfish, which has a drastically streamed-down genome (it has removed most transposable elements and some genes--its shortness made it an attractive target for sequencing). It is thought that TLR4 may have another purpose in fish, since it does not appear to respond to endotoxin stimulus in the same fashion as in mammals. (Iliev, D. B.; Roach, J. C.; Mackenzie, S.; Planas, J. V.; Goetz, F. W. "Endotoxin recognition: In fish or not in fish?" FEBS Letters 2006, 579, 6519.)
This is something that is seen often throughout evolution--a gene used for one purpose eventually takes on a new one. We see the same thing with olfactory genes, many of which are expressed in sperm cells and probably used for chemotaxis.
Additionally, TLR4 is not present in corals, which contain an ancestral TLR prior to radiation into the chordate TLR family.
(Found here.)
As you can see, the ray-finned fish evolved from the paleoniscoids, while tetrapods evolved from the crossopterygian fish. The tetrapodian line of descent did not go through the ray-finned fish.