I will try to answer your question, but I do not know Indonesian. :) "Thank you for your visit" is more common than "Thank you for your coming." Instead of "Thank you for your coming," we would usually say "Thank you for coming." This is more common in everyday speech than "Thank you for your visit." The last sentence is a little more formal. None of the sentences have a "negative connotation," unless the speaker has a different meaning of "coming" in mind (which refers to sex). I can say, "Thank you for your coming so far through the bad weather to visit me." This has no negative connotation. The difference is only one of grammatical construction: Thank you for (your) coming. => uses the gerund "coming" after the possessive pronoun "your." You can also just say: Thank you for coming. => here the "you" is understood to mean the person to whom you are talking. It has the same meaning as "Thank you for your coming" and is more common than "Thank you for your coming." Thank you for your visit. => uses the noun visit. Summary: "Thank you for coming" is a very common way to thank someone for visiting you. "Thank you for your visit" is a more polite and slightly more formal way to say the same thing. "Thank you for your coming" is not used often.