Hmm, good point. I would guess that Aereo, etc. may remove commercials, à la TiVo, during post-processing. Or even more rudimentarily, allow seeking, e.g. fast-forward over commercials.
Aereo doesn't post-process. It just forwards the content of a miniature antenna to your device over IP. There's a one-to-one mapping between viewer and antenna.
Cable companies, by contrast, currently tap the main feeds at one point, rebroadcast the content to their subscribers, and pay retransmission fees to the broadcasters.
(Aereo also operate a DVR service, but the big fight is over the retransmission fees they're not paying)