But this thing about ignoring Sisko isn't unusual, people normally name things in threes and Kirk, Picard and Janeway are the three best known captains. It's like that book Steven Colbert read on that famous episode of his Report ("Only god could love Star Trek Voyager"), it only mentioned those three as well.
I gather the commercial didn't name things is threes, but in pairs of twos, so I think we can leave that argument aside.
As for the Colbert example, I didn't catch that episode of the Report, so I probably shouldn't comment on it

But it doesn't sound all that similar. It sounds like the two main references (Kirk and Picard) were being used to mock a third (Janeway).
In the case of the commercial, the intent was to establish that ENT was carrying on the Star Trek legacy, so I think we can infer that the character choice was made with that in mind.
The pure popularity argument doesn't stand up to much scrutiny anyway, since Seven of Nine, Data, McCoy and Scotty (at least) would almost certainly have trumped Janeway in that regard. Janeway's popularity with regard to Sisko at the time is debatable to say the least, as DS9's ratings were always better than Voyager's.
So we can basically assume that the choice of the four characters were just the first four that came to somebody's mind (unlikely), or that they were the result of some sort of bizarre calculation whereby it was going to be 3 captains + Spock and somehow it was ascertained that more people knew and cared about Janeway than Sisko even though more people watched Sisko's show than Janeway's show.
Or we can suppose that Sisko was left out initially because DS9 was not perceived as part of the legacy that ENT was continuing, probably due to the notion (still floated from time to time) that DS9 was not really Trek because it was not mostly focused on exploration and not sufficiently optimistic. That doesn't make it some kind of major scandal, but that explanation is at least as plausible as any other explanation.