Where there is no smoke, there is no fire.
I don't watch the news and avoid right-wing sites, so I don't remember ebola being used as a weapon against Obama. The media coverage I remember, just not the part about Obama.
Still, I don't think you can make the case that zika is being downplayed compared to ebola and also recognize that zika is hardly the threat ebola was. Since zika is a much smaller threat it stands to reason there is less worry and news about it.
I'll grant you the political what-ifs in the South are intriguing.