Setting aside the illegitimacy of the SCAF, there are numerous other reasons. Even if our rulers were legitimate, they have an obligation to respect human rights, democracy and the Egyptian vote. The military have disrespected the referendum and provide no reason for us to believe they will respect our votes in the election. The SCAF seemed to have killed their own people in order to force 'democracy' down their throat. If the will of the people had any weight, elections wouldn't have taken place after the police murdered numerous unarmed protesters.
Even if we set aside attitude, for elections to be legitimate they must be agreed on by the Egyptian people. The people were never asked, and when they voiced out their demands, they were never heard, and even when they were heard, they were never listened to and never was any action taken. So what we have here are elections put forth by a dictatorship that does not respect the various opinions of its citizens; could such a dictatorship ever respect their votes? Furtheremore, it is difficult to convince yourself or anyone that these elections have any legitimacy when half the people are afraid to go out and vote due to justified security reasons.
How can those brave voters be accountable for their vote? Where, when and how has information regarding the elections, the rules and the candidates been made available? Most voters are placing their votes as they do with bets on a roulette table. It is a complete gamble due to the murkiness of the electoral process and the availability of information.
Setting aside all the above, even if parliament were formed without rigging, it would be impotent. They have no power to fulfill their promises and they would be used as a front for SCAF. People are to direct all their anger towards the powerless parliament. This makes the future parliament illegitimate because it will fail to represent the people.
Voting or boycotting will not change the illegitimacy of these elections. It is enough that a great number of people feel that the laws are not fair and that the time isn't right and that the rulers are biased towards their self-interest. You may vote to lessen the blow and you may boycott to prove a point, but that isn't the real crux of the matter. So if to vote or not to vote is not the question, what is?
The real question is whether you're selling out. Neither action determines that. People have died for democracy, and democracy isn't unfair elections. Democracy means justice, respecting minority rights, respecting human rights and allowing others to take part in the decision making process. We haven't had democracy yet, and so the votes won't matter. We can't have elections and democracy as the junta and police kill protesters and disrespects citizens. How will a vote be respected by these people if a human life is not respected?
These elections are not what people died for. There is no honor in accrediting something as farcical as these elections to their death. The important thing is to remember what they died for. They died for bread, freedom, social justice and dignity. There is no dignity in running rapidly like a rat through a fore drawn maze. You don't sell out by voting or boycotting, you sell out when you settle for less than what thousands have died for.