Why is Thermus aquaticus and Taq Pol stable?
Here is an article from Razvi and Scholtz that help you understand the thermostability found in thermophilic proteins. They compared protein stability of thermophilic proteins and their homologous versions in mesophilic bacteria (i.e., bacteria that grow in more normal temperature ranges), and compiled these proteins into a database. Their method was to make estimates of protein stability curves for each of these proteins through a model of free energy based on the known physical parameters of these proteins. From the article: 


  [...] the most common way to attain a higher [melting temperature] in proteins from thermophiles is to raise the stability curve to higher values of ΔG (higher intrinsic stability) at all temperatures."


This is achieved through mutation of just the linear sequence of the protein. Fundamentally, 


  "...each of the methods of stabilization are results of features like an increased number of hydrogen bonds, salt bridges, improved core packing, shorter and/or tighter surface loops, enhanced secondary structure propensities, or oligomerization."


Also, everything I have seen about the genus thermus places them as Gram negative bacteria.


Razvi and Scholtz. Lessons in stability from thermophilic proteins. Protein Science, 15(7) 2006.