With the current situation with the DB and the problems on the Hannover-Berlin track, it is probably best to fly especially if it is more time critical. I regularly commute between Frankfurt and Berlin and I usually take the train but right now flying may well be more convenient and practical.
As pointed out by the previous posters, TXL is not the problem but the can be quite some queues at security in FRA and on a Monday morning it can be a real pain. On Saturday mornings it shouldn't be a problem though.