I'm no fan of Thaksin (maybe you heard?) but this should not be made into something it is not. It's a long standing football tradition for fans to put up flags as banners. Often that will be an English flag (the cross of Saint George) or a Union Jack or the national flag of the player or hero in question.
Fans like to express their allegiances. At England games, the fan flags will often have the name of the fan's local team written across the middle. This is particularly popular with supporters of smaller teams.
Otherwise the name of the team's star player will be written across the flag. Sometime fans go further with their merchandise. For example, during the nineties when Uwe Rosler was a star striker at Manchester City, City fans had T-shirts bearing the slogan "Uwe's grandparents bombed Old Trafford".
The three banded Thai flag (nation, religion, King) would certainly not be disrespected by City fans and surely expatriate Thais would be well aware of the consequences of such an action. It pains me to say it, but I think Noppadon is correct in saying this is the actions of westerners who simply did not realise there was a big cultural issue at stake.