Your problem is largely due to using symmetric colors. The other thing to consider is using manual color breaks. See the answer from "Lippy" here for an example of how to change these.

The problem is with your range of values that's why on the either ways to zero its 1;9 and then you scale columns, try with scaling rows and add breaks in your heatmap command as;

breaks=c(-0.1,0,0.2,0.3,0.4,0.5,0.6,0.7,0,8,0.9)

or better to plot a heatmap of z-score and use colors from RColorBrewer

e.g. I would do in this way

library(gplots)
library(RColorBrewer)
hr <- hclust(as.dist(1-cor(t(Gene), method="pearson")), method="average"); 
hc <- hclust(as.dist(1-cor(Gene, method="spearman")), method="average")  
# Cuts the tree and creates color vector for clusters.
mycl <- cutree(hr,k=4, h=max(hr$height)/1.5); 
mycolhc <- rainbow(length(unique(mycl)), start=0.1, end=0.9)
mycolhc <- mycolhc[as.vector(mycl)] ; myheatcol <- bluered(75)
heatmap.2(as.matrix(Gene), Colv=as.dendrogram(hc), 
          col=myheatcol, scale="row", density.info="none", 
          trace="none", RowSideColors=mycolhc,cexRow=1.5, 
          cexCol=1.5, keysize=1,margins=c(20,10))

hth