The new flag
The Commission in charge of creating the new flag gave a very fragile justification for the choice of colours. They based their arguments in a symbolic reading, rather then heraldric principals (which were very fragile, as I showed in post above). According to the official explanation, the red was chosen for being the militant colour par excellence (since it remembers the blood and it inspires feelings of victory), while the green would be the colour of hope.
The truth, however, is that they were colours without great historical tradition (some scholars say they were related to the colours of two major military orders – the Order of Christ, whose cross was red, and the Order of Avis – but I doubt the Republicans were considering that, when they chose the red and green…) and, as we can see, hardly could the Commission justify its inclusion in the Flag.
It seems more plausible that the two basic colours were related to the Carbonari (a secret, revolutionary society that flourished in Italy, France, Portugal and Spain early in the 19th century, in the fashion of the Freemasonry), since green and red are the colours of the mantle that covers the image of Saint John the Evangelist, the patron of the Carbonari (and that’s why they are also the colours of the Italian flag).
About the partition of the two basic colours, I believe this ratio was also related to the flag of this secret society, since the Carbonari’s flag was 2/5 red and 3/5 green, while the Portuguese flag is 2/5 green and 3/5 red...
(As Danny says however, the monarchic blue & white flag, in its version for naval use, had already a 1/2 partition, while the flag for terrestrial use was equally divided. I don't think they are related though, since they were different partitions, but I'm not an expert)
The link provided by Kelly9480 is preciselly about the right proportions and it exemplifies how the Portuguese shall not be represented.
Besides this choice of colours, the Commission also decided to keep, in the essential, the same representative emblems of the Nation that already appeared in the previous blue & white flag. For the lovers of heraldry, these are truly the important symbolic elements, since the historical continuity of the Nation is represented mostly in there, rather than in the colours.
Here’s a brief resume of those symbols, which were basically the ones transferred from the blue & white flag to the red & green one, except for the crown (that was eliminated in the second flag, for obvious reasons):
1. the yellow/gold armilla (esfera armilar), which was adopted as the personal emblem of D. Manuel I, and is present in the national emblems since then. It symbolizes the Portuguese Discoveries and the most shining period of our History;
2. the white/silver shield sprinkled by the blue shiels (quinas), each one with five silver beasants (in memory of the five sore of Jesus Christ that, according to the legend, appeared in a vision to D. Afonso Henriques, during the first battles for the Portuguese nationality);
3. a crimson wide band that surrounds the white shield, over which are placed the seven yellow/gold castles (which represent the Muslim kingdoms the Portuguese had to fight in the beginning of the nationality).