Yes, they are actually equal... well, sometimes.

Dominance is irrelevant here. "Dominant" doesn't mean "more likely to be inherited." A dominant allele is one that gives you its distinctive phenotype when you inherit just one copy. A recessive allele requires you to inherit two copies before you have that phenotype. That's all. [1] The Punnet square works the same whether the alleles are dominant, recessive, incompletely dominant, or whatever.

Each axis of the Punnet square represents the two homologous chromosomes of one parent's diploid cells. When that cell undergoes meiosis, the homologous chromosomes are separated. One goes into one child cell, and the other goes into another. So each of those chromosomes is present in exactly 50% of the gametes. The same is true of the chromosomes in the other parent. So if you're heterozygous at an locus that codes for something like purple vs white flowers or something like that, half your gametes will have each allele. And if your partner is too, half their gametes will have each gene.

For the purple/white flower gene, that also means exactly 25% of your offspring will have each combination. One gamete at random from each partner. It doesn't matter whether the purple flower gene is dominant or incompletely dominant or whatever.

If the difference between the alleles is something more serious -- for example, not purple vs white flowers, but whether or not you successfully gastrulate -- the allele frequencies in the offspring are going to diverge from 50/50. This is evolution through natural selection. If the "can't gastrulate" allele is recessive, you won't see 25% of descendants in each quarter of the Punnet square. In fact, 0% of the offspring will be homozygous for the "can't gastrulate" allele, because they all died as embryos. However, if we observed the embryos at the moment of fertilization, there would still be 25% of each.

Sometimes natural selection happens before fertilization too. If an allele makes your gametes not work so well, those gametes will be less likely to even make it to the point of generating an embryo. For genes like this, the 50/50 model of the Punnet square kind of stops working. When you think about it, this kind of allele might actually be pretty common. Gametes don't just do gamete-specific stuff like making flagellae. They also need to do normal things like transporting glucose into the cell, and if they are worse at any of these normal things, they're probably less likely to succeed at being gametes. On the other hand, they probably don't even express the gene for flower pigments, so that one is probably truly 50/50.

[1] In reality, a lot of alleles aren't really 100% dominant or recessive. If you are heterozygous, you may get a phenotype that's somewhere in between the homozygous phenotypes. Sometimes it's exactly halfway between, but it is often very close to one side or the other, and those genes are considered dominant and recessive, even if they aren't truly 100% dominant or recessive. But none of this is relevant to the frequencies in the Punnet square.