The case bottom is part of the heat dissipation system it is supposed to heat up and should not be blocked. Don't use it on pillows or a blanket and, if you must use the computer in your lap, use a lapboard to insure air gets under the case.
"Hot" to the touch does not translate to "too hot for safety." If you have heat concerns, you must get a utility that tracks the temps of the various internal bits. I like this widget:
http://www.apple.com/downloads/dashboard/status/istatpro.html
For the MBP models covered in this forum (silver keys), the system will shut down when the processor temps approach 100G/212F. With Flash web apps, mine run in the range of 145-160F, where normal use runs around 125-130F.