Why are measure words sometimes omitted? For example, "我有房子", but why not "我有一栋房子"? Why "我有孩子" and not "我有一个孩子"?
Why "我不是坏人" and not "我不是一个坏人"?

Thanks
Your first two examples are not proper ones, since Chinese grammar do not usually use plural or singular form, 我有房子 could mean "I have a house" or "I have houses" ; 我有孩子 could mean " I have a child" or "I have children".  

As for the third example, 我不是坏人, since 坏人 is a description word for the subject, no matter the subject is singular or plural, therefore, classifier is not needed.

The subject can be 我，我們 or 我們三個,

我不是壞人

我們不是壞人

我們三個不是壞人

in all three cases, 壞人 does not require a classifier 


if you write 我們三個不是(三個)壞人 , the second qualifier (三個 ) would be redundant, we know it is three from the subject 我們三個
if you write 我不是(一個)壞人, (一個) would also be redundant, we know it is one from the subject 我
if you write 我們不是(兩個/一群)壞人 ,  (兩個/一群 ) would be redundant, we would know the subject is "two people" or "a group of people" from previous context.


Although writing "我不是一个坏人" is not grammatically wrong, keeping your writing as direct and as simple as possible (for example, omitting subject, object whenever possible) is considered good form of writing by most writers.