According to http://starling.rinet.ru, they come from different Proto Indo-European roots. The database is based in the Indo-European Etymological Dictionary project.
- aequus would come from *aikʷ-, meaning flat and also present in Baltic languages such as Lithuanian.
- equus would come from *ek'w-, meaning horse, properly. Hippos comes from the same root.
I'm no Proto-IE expert, but apparently these are regular transformations, and it is nothing but a coincidence (or, at most, an example of convergent evolution).
Caveat: since Proto-IE was never written, all we have is a theoretical reconstruction, mostly agreed by scholars (and thus reliable enough for modern-day purposes). That is why roots always start with an asterisk (*): they aren't properly attested. Maybe if we travelled back in time we'd be surprised.