Given the money the US military has (equal to 50% of the entire Russian economy), you'd sure think they could afford to throw whatever was necessary at improving security for Trump's iPhone situation. I suspect the point of an article like this, which is an off the record leak of internal information that wasn't authorized, is to get Trump to abandon the iPhone period. I don't think these insiders want to bother with trying to increase the security for how things are now (they may view it as very impractical), they're seeking to embarrass Trump into changing behavior (good luck).

Or why not use a VOIP like protocol with end to end encryption like WhatsApp or telegram ?

Because that requires buy-in by the person you want to call. And Mr. Trump wants to call whomever he wants, whenever he wants; he's not going to wait for his staff to arrange for the other person to install WhatsApp.