Now the real struggle for Egypt begins.

In round one of Egypt's first free elections, Islamist parties strongly outperformed the others. Two more rounds of elections will take place by mid-March, but the message of the first round couldn't be clearer.

Egypt's political landscape will be dominated in the near term by parties with strong Muslim religious leanings. For all those who are concerned about this outcome, it's important to understand what this does - and doesn't - mean.

Egypt is not Iran. The people of this predominantly Sunni Muslim country do not believe in rule by clerics. Egypt's Facebook revolt in Tahrir Square was organized by youths who believed in a civil, not a religious, state.

So why did the Muslim Brotherhood, via its Freedom and Justice Party, do so well at the polls?

In part, because the Facebook rebels proved unable to translate their skills into campaign operations. They continued to rally in Tahrir Square, but failed to organize effectively for elections, rather than creating a broad political coalition. They had no charismatic leaders with name recognition, and no clear platforms. Also, the large numbers of parties and the complicated voting system confused first-time voters.

The Muslim Brotherhood, on the other hand offered a recognizable brand name. And for many traditional Muslims, the idea of a "good Muslim" getting elected to office was comforting; the concept of civil (secular) parties was misunderstood, with the term secular misinterpreted as hostile to religion.

When I visited Cairo's working-class Imbaba neighborhood in November, many locals told me they would vote for the Brotherhood party's candidates because they were "good people who did good things for the poor." Similarly, the more fundamentalist Nour Party of Salafi Islamists, which finished second in many districts, also garnered popularity by its charitable work.

Long banned from politics, the Brotherhood gave up violence and focused on social work. It developed a tight organizational structure all around the country and gathered thousands of loyal followers. It provided a steady stream of funds to the religious organization (as did Arab gulf countries). This gave it a great monetary advantage over nonreligious parties.

Once its party was legalized, the Brotherhood's cadres of veiled women and youths got out to vote. Its computerized operations weren't unlike those of machine pols in the wards of Chicago or New York.

However, despite its success in the first voting round, the Brotherhood's ultimate strength is still uncertain until the voting is entirely finished. Moreover, it is hardly the only political player in the new Egypt. It is still pitted in a three-way struggle with the ruling generals (known as the Supreme Military Council, or SCAF) and with those Egyptians who support a "civil" state. The latter include non-Islamist political parties, along with civil-society organizations and human-rights groups.

Egypt's political future will depend on how that struggle plays out.

The SCAF generals initially felt more comfortable dealing with the Brotherhood than they did with the Facebook rebels or civil-society groups. The latter were critical of the military's human-rights violations and were less easy to control than the Brotherhood - or so the generals thought until very recently.

Now, the SCAF is rethinking, but not seriously enough.

The generals want to keep their perks and power even after the elections are over. The Facebook rebels and civil-society groups urged the SCAF to appoint a strong civilian interim government during the election transition, which would have offset growing Islamist power. But the generals refused. (They just appointed another weak member of the old guard as prime minister.)

This rejection - and the military's war on civil society - has played into the Islamists' hands.

Buoyed by their first-round victory, the Brotherhood's party is insisting - in opposition to the military - that the new parliament should choose the interim government. It is also insisting that the parliament must choose all members of the committee that will write the new constitution; in a parliament dominated by Islamist parties, that bodes ill for Egypt's future.

The generals have a choice:

They can appoint a strong independent champion of a civil state such as Nobel laureate Mohamed ElBaradei to be interim prime minister, and hand over real power. This would provide a strong civilian counterweight to growing Islamist strength.

Or the generals can stick with their present course, and watch their power diminish as elections give the Islamists political legitimacy as the strongest political force in the country. Unlike its treatment of civil society, the military dares not attack the Islamists with guns, lest they bring a million followers out on the streets.

To retain their legitimacy, the generals will have to concede some of their power. But the time for making that decision is running out.

E-mail columnist Trudy Rubin