A few things.
Firstly, don't download and compile these, just install the packages from the Ubuntu repository.
sudo aptitude install pscscd
You should already have libusb, but you could install that much in the same manner.
Now that that is solved, let's pretend you did
want to build that software. Running ./configure will generate a Makefile (sic) using automake. So, you want to just run the make command, without -f Makefile.in, which is not meant to be invoked directly. Makefile.in and Makefile.am are used by automake to create an actual Makefile (sic). The phrase @SET_MAKE@, for example, is not something that will be comprehensible in the make syntax.