I hope you are not misinterpreting the data, there is no scope of transmission through latex. On the contrary, it is estimated that there is approximately 2% possibility of failure due to breakage or slipping when used incorrectly. Some possible red flags are using 2 condoms together, using oil based lubricants, using a condom with out removing the air etc.
Therefore, when it is used correctly and consistently it protects against HIV transmission.
No product will ever be free of failures. My understanding is that the 98% rate for the condoms come from the fact that condoms sometime break or slip off. Don't worry, though, as long as your condom remain undamaged you should be safe. The other reason why companies say that condoms are only 98% safe is because they want to avoid potential liabilities.