In reality Pangaea had broken apart long before the time Terra Nova is set (a map of the continents 94 million years ago can be seen here, and a virtual globe showing the continents 80 million years ago is here), so the logo shouldn't necessarily be taken as a literal representation of the Earth of 85 million years ago (though the final shot of "Occupation-Resistance" suggests it probably is intended to be what Earth looks like on the show, see the discussion below). As discussed in this article, early promotional materials for the show made reference to it being set on Pangaea (as does this page on the first concept drawings from an early production designer, and this November 2009 script draft which also has the colony 154 million years in the past rather than 85 million) but references to Pangaea were deleted from later promotional materials, so this seems to represent an idea that was scrapped. Perhaps by that time the logo had already been designed and producers didn't think it was worth changing in the name of accuracy. (You can see the logo is at least as old as this article from May 2010, where it was reported that the show would be set 150 million years in the past rather than 85 million. Also, this article was only three months after one of the first reports that Spielberg was in negotiations to produce the show, in February 2010, so the logo must have been fairly new in the May 2010 article).
A tweet from InsideTerraNova says, "Our show takes places during the Cretaceous period, many millions of years after Pangaea broke into continents." Presumably this would not have been mentioned unless the idea was that this was true in the world of Terra Nova too (see the Science & Speculation section of The Probe for a discussion of how Terra Nova might take place in an alternate time-stream that only branched from ours at the moment the Time Portal appeared, so that the arrangement of the continents would be the same as in our own past).
At the end of the season finale "Occupation-Resistance", a shot of the prehistoric Earth is shown, and it shows a landmass that appears quite similar to Pangaea. But it is not quite identical to the Pangaea that appears in the show's opening, as can be seen in the comparison below; the shape of the coastline is somewhat different, the bottom section of the Pangaea of the opening appears fatter (though the bottom section on the logo is thinner than the one on the animated version in the opening), and there seems to be a large island off the coast in the finale that isn't seen in the version from the opening. Most likely these are just minor tweaks to the Pangaea of the logo to give it a little more detail, but perhaps the differences leave open a slight possibility that the landmass seen at the end of "Occupation-Resistance" actually consists of two continents, like North America/South America or Eurasia/Africa, although the shapes don't seem to be a good match with the prehistoric maps from 94 and 80 million years ago linked above.