configure is (usually) a shell script that checks your system for all required features before building anything. Makefile.in is a template for a Makefile. The results of the configure tests are substituted into Makefile.in to generate Makefile. This is to deal with people having things (compilers, headers, libraries) in obscure paths, cross-compiling (e.g., building for ARM on x86), optional library support (some programs have additional features that can be switched on or off), compiling with different options, and so on. Writing a one-size-fits-all Makefile is actually really hard.