Mozilla is an organization that prides itself on openness and equality, on being inclusive as an organization and a culture. This is reflected in its products, in many different ways—all of them good, generally speaking.
The CEO is the figurehead of a company or organization; they have to represent the company, establish its culture, define its vision, and so forth and so forth.
Having a CEO who has a history of donating to an anti-equality campaign, an act that very strongly suggests having an unequal view of certain groups of people (LGBTQ folks in this case), does not mesh with an organization that prides itself on equality (among other things). They are pretty mutually exclusive.
It was already a conflict with Eich as CTO, but at least in that position he had no say over the company culture or its policies when it comes to people, just technology. As CEO, all that changed.
Additionally, by making a donation to (what is essentially) a campaign of hatred (and FUD), he took it WAY beyond a personal belief or view. Expressing your views in public or making a donation that way is an act, not merely "holding an opinion", and actions matter. His action in the form of the donation harmed the lives of thousands of people, with no justifiable cause for it.
Now, there's tons of people who hold such bigoted views and even express them in the form of acts through public statements or donations, but most of the time we don't award those people with the CEO position of a major corporation.
(to clarify how this is not a litmus test: while it sure can be applied that way, plenty of organizations have bigots as CEOs — see e.g. Chick-fil-A — but what’s mainly happening here is that it is simply a matter of bad judgement and people objecting to the appointment because he's unfit to lead an org like Mozilla)