No, they're NOT.
Maybe they're equal in an wishful ideological world in that all authoritarian governments are equally evil. That's a given.
But in Realville, Egypt, the two sides are not equally evil. The Muslims are on fiery, murderous rampages in the Christian communities as we speak. The military is not targeting Christians...only the Brotherhood terrorists.
The military will not tolerate the Muslim religious savagery such as beheadings, suicidal bombings, stoning and other abuses of women, etc. They have no history of this.
The Egyptian people simply want to get back to normal. For instance, being a nation of many shopkeepers and small entrepeneurs, these citizens want to get back to work so the tourists eventually return. A huge hunk of Egypt's economy depends on tourism.
Do you think the tourists would EVER return with the Muslim Brotherhood and Sharia law in control? Believe me, they'll take the Generals' interim governance any day over that of perpetual despotism by crazy Imams and their violent cultist followers.
No, the two sides may be not be to the liking of the free world, but only one is going to come out on top....and you can't use moral equivalency to put them in the same category, because they're not in this particular case.
Therefore, at this point, we are wise to side with the military, or at the least, keep our snoots out of the fray. The military will prevail in the long or short run, anyhow, you can rest assured.
Leni