Why does not GCC compile the C99 by default? I mean why is it necessary to add --std=c99 flag everytime a code in C99 is written?
The reason is that default configurations of gcc take a really long time to be changed, since every time a default configuration is changed, it can potentially break the compilation of valid programs (in this case valid c89 programs which are invalid in c99). Starting with gcc 5.0, the default C standard used by gcc will be gnu11, which is c11 with gnu extensions (see here):
The default mode for C is now -std=gnu11 instead of -std=gnu89.